Which temple is meant in Daniel 9:26-27?
In the New Testament, the Jerusalem temple was a type and shadow of heavenly or spiritual things. Jesus identified himself with the temple. The apostle Paul wrote to the Corinthian church, “Know ye not that ye are the temple of God, and that the Spirit of God dwelleth in you?” [1 Corinthians 3:16] And similarly, he said, “What? know ye not that your body is the temple of the Holy Ghost which is in you, which ye have of God, and ye are not your own?” [1 Corinthians 6:19]
When we consider Daniel’s 70 weeks prophecy in the light of the gospel, the question arises, which temple is made desolate, the earthly one made with hands, or the heavenly, spiritual one that Paul referred to? The heavenly one is the church.
Most expositors assume that the temple referred to in the 70 weeks prophecy is the earthly temple, the one that was made with human hands, and the city is the earthly city of Jerusalem. The question, which temple and city the prophecy applies to, is seldom addressed by expositors.
German theologian K. A. Auberlen (1824-1864) commented on Daniel’s prayer of confession, and he alluded to the claims by critics who denied that the prophecies of Daniel were authentic, that they were written during the second century BC. He wrote: 
Our chapter places us in the first year of Darius the Mede. If, as is still more probable, we are to understand by this Darius, Cyaxares II., in whose name his nephew, son-in-law, and successor, Cyrus, as commander-in-chief of the entire Medo-Persian army, conquered Babylon, 538 b. c., then the date of our chapter would fall about the year 537 b.c., nearly a year before Cyrus gave the Jews permission to return from their exile, and sixty nine years after Daniel had been carried away to Babylon at the commencement of the captivity, 606 b.c.
We can easily understand why the pious Israelite, who so sincerely loved and clung to Jehovah and his nation, should feel himself moved at this time to make the prophecy of Jeremiah concerning the seventy years, which were to witness the desolations of Jerusalem, the object of his investigation and earnest reflection. But he investigated the Scriptures with prayer. He poured out his heart in ardent supplication before the God of the Covenant, and cried to Him to vouchsafe His mercy to the people who were called by His name, and to restore the sanctuary and the city. This is one of those biblical prayers where we feel that it is not by human exposition that we can enter into its meaning, depth, and significance, but that the words must explain themselves in our own hearts. Daniel, the just and faithful servant of God, enters so deeply into the guilt and sin of his people, in the consciousness of his priesthood he identifies himself so entirely with it, he repents so heartily in the name of all Israel, that we feel here a presentiment, as it were, of what happened in the inner sanctuary of the atoning substitution, and our view is borne aloft from the chamber of Daniel to the prayerful sacrifice of Gethsemane and Golgotha. As we have seen above that, in general, the prophet’s own life forms the typical substratum for his prophecy, so also in this particular case his own experience forms the typical starting-point of the prophecy concerning the perfect atonement for sin. In this prayer of repentance, Daniel is a type of that highest Priest who was to be cut off (ver. 26), and should thereby cause the sacrifice and the oblation to cease (ver. 27), because He Himself has made reconciliation for iniquity and brought in everlasting righteousness (ver. 24). Daniel was especially prepared to receive this revelation of the New Testament priesthood, at the very time when he himself had appeared before God in his priestly office. And can this prayer, which it is not possible to read without deep emotion in the very heart of hearts, be a cunning deception? It only shows how much our criticism is devoid of a deep and earnest sense for religious truth and truthfulness, when to such questions it attaches so little importance.
The prophecy is contained in four verses, which as Auberlen pointed out, “contain angelic language.” This, he said, accounts for the difficulty that interpreters have had explaining them. He said no one has managed to clear up the obscurities in the message. The confusion has only increased, since the time of Auberlen. He wrote: 
Before we proceed to consider the revelation which was vouchsafed to the prophet in answer to his prayer (ver. 24-27), let us remind the reader, first of all, that these four short verses contain angelic language; they are in the style of the upper sanctuary. Hence it is so difficult for us impure men (Is. vi. 5) to enter into their meaning; and hence there is no interpretation which has completely overcome the difficulties and thrown clear light on the obscurities in this angelic message. The answer naturally refers to the question, the favour shown to the petition offered; though the divine answer extends far beyond the human question, and the divine favour transcends all that we can think and pray for. We must endeavour, therefore, to enter vividly and fully into the thoughts and feelings which form the basis of Daniel’s prayer, in order to understand as far as possible the words of the angel.
Auberlen’s comments contrast with the following comment by J. B. Coffman: “There is not a single word in this prophecy that is not disputed; and we shall note some of these opinions; however, in the overall sense, there is not anything very hard about this prophecy.”  But Coffman’s approach seems simplistic. Auberlen wrote: 
Daniel prays for the liberation of Israel, and for the rebuilding of the city and the sanctuary. He prays for this manifestly in view of those great promises, whose fulfilment was connected with this event. For in all the prophets, especially in Jeremiah, who is more especially present to his mind (Jer. xxxi.), the fulfilment of the Messianic hope was inseparably connected with this restoration. The revelation which Daniel himself had received in the second and seventh chapters, showed him doubtless that the Messianic kingdom was not so immediately near, in its glory at least, since but one of the four universal monarchies had passed away. But this made it the more necessary that some explanation should be granted him concerning the prophecies of the earlier prophets, in whom he saw an intimate connection between the deliverance from captivity and the Messianic salvation. The revelation now vouchsafed to him has for its purpose to analyse into its successive parts that which the prophets, according to the law of prophetical perspective, have hitherto seen together in one, viz. the redemption from captivity, and the full Messianic redemption. It had indeed occurred more than once in the Old Testament, that there were relative fulfilments of earlier prophecies, and that it became necessary to warn the people not to trace in them the highest and absolute fulfilment. The pious servants of God under the Old Covenant, who longed for the consolation of Israel, and who, like Noah’s father (Gen. v. 29), hoped many a time that now the Comforter of their afflictions was nigh at hand, have to wait from age to age, and to view the preceding fulfilments only as pledges and earnests of the coming of Him whom they desired so earnestly to see (Matt. xiii. 17); just like those Christians who believe the coming of their Lord to be near, but are ever expected to continue waiting. Thus David comes as a relative fulfilment of the older promises, but Nathan the prophet was sent to announce to him that he was not to build a house to God, for that God would build a house to him, and that his seed was destined to be the mediator of Jehovah’s true dwelling among His people (2 Sam. vii.). In like manner in our prophecy—and we know that this is in accordance with the essential characteristic of the Apocalyptic—Daniel receives the intimation of a long period of seventy prophetic weeks instead of seventy years, at the end of which the expected salvation would come; and thus the time is indicated which would elapse between the nearer and relative fulfilment, and the further and absolute, from the issuing forth of the commandment to restore and to build Jerusalem, till the time of the Messiah. As the Lord answered Peter’s question, “Is it enough that I forgive my brother seven times?” with, “Not seven times, but seventy times seven” (Matt, xviii. 21, etc.); so the angel here answers Daniel, not seventy years, but “seven times seventy years are determined upon thy people, and upon thy holy city.”
Since Daniel’s prophecy directly quotes the words of the angel Gabriel, is it wise to assume that the sanctuary in verse 26 is a temple made with human hands, one that was merely a shadow and a type of the real one? The tabernacle in the wilderness was made according to the pattern of heavenly things. [Hebrews 8:1-6] Similarly, the temple of Solomon, and the temple of Zerubbabel, built after the Jews returned from exile, were built after the same pattern, and so were “shadows” of things heavenly, and spiritual. What sanctuary, then, is meant in the message of the angel in Daniel’s prophecy?
In the angel’s words, “after threescore and two weeks shall Messiah be cut off, but not for himself,” for whom was he cut off? Isaiah wrote: “But he was wounded for our transgressions, he was bruised for our iniquities: the chastisement of our peace was upon him; and with his stripes we are healed.” [Isaiah 53:5]
The New Testament identifies both the “city” and the “sanctuary,” (or temple) with the church, those for whom Christ was cut off. In verse 26, where the “city” and the “sanctuary” are destroyed by the people of the prince that shall come. This must refer to the real sanctuary, rather than its type, or shadow. Applying the words of the angel to the shadow misses the true significance of the prophecy. Why would an angel of God have been sent to reveal the future destruction of a mere shadow, or a type, that in Daniel’s time had not yet been built? The real sanctuary is the church.
Daniel said of the prince, who opposes the Prince of princes, “And his power shall be mighty, but not by his own power: and he shall destroy wonderfully, and shall prosper, and practise, and shall destroy the mighty and the holy people.” [Daniel 8:25]
The saints are the “sanctuary” described in Daniel’s prophecy. The Jewish temple, made with hands, was destroyed in 70 AD, but no flood was involved. Its destruction has obscured the significance of Daniel’s prophecy. The desolation of the church, however, has an immense significance for our understanding of the gospel and the history of church.
Each of the things that were to be accomplished within the 70 weeks, mentioned in verse 24, pertain to the gospel. This fits the view that the temple and city that Daniels’ 70 weeks apply to is the church, of which the earthly city and temple were types and figures. The atonement and forgiveness of sin, bringing in of everlasting righteousness, etc., are accomplished in the last week, after the coming of the Messiah. Auberlen recognized that everything mentioned in this verse have to do with the gospel. He wrote: 
The twenty-fourth verse belongs to the most profound and glorious passages in the Old Testament; and if anywhere these have a Messianic signification, it is here. The angel wishes at first to give the prophet the general impression that his hopes and prayers for the Messiah will be fulfilled in a much later period than he expected. The seventy years of exile were indeed, as he had confessed in his prayer, a punishment for the sins of the people, yet not a perfect satisfaction for them before God. God would certainly visit Israel with His redeeming mercy, but the full atonement and forgiveness of sin, the eternal and everlasting restoration of the normal state between God and sinners … would come only after seventy prophetic weeks … the angel presents to the prophet in these expressions a connected chain, each link of which bears, upholds, and explains the other, and which, taken aggregately, represents the Messiah as the perfect sin-offering of the covenant, a revelation which Daniel, an earnest investigator of Scripture, could find more fully explained in the fifty-third of Isaiah.
Auberlen saw that these could only apply to the heavenly sanctuary, which is the New Testament church, referred to as the new sanctuary below: 
In this time of salvation, Gabriel continues, not only the prophecies of Jeremiah, but likewise all visions and prophecies in general will be fulfilled (Luke xvi. 16; 2 Cor. i. 20); and not only will a new sanctuary be dedicated as Daniel prayed, but a most holy place where God would dwell with His people in a peculiar manner (John ii. 19-22).
Daniel’s prophecy foretold the coming of the Messiah, and his offering as the atonement for sin. Auberlen wrote: 
The most prominent thought is this: Even as, and because at that time the perfect sacrifice will be offered as an atonement for sin, the holy presence of God will likewise be perfectly manifested (Ex. xl. 9, 34). For only when sin is altogether taken away can God be really and perfectly present.
Thus the fundamental idea of our verse is, that the seventy years of exile are only a type of the farther seventy prophetic weeks, and that the redemption from captivity at the end of the seventy years is, in like manner, but a feeble type of the full Messianic redemption at the end of these seventy prophetic weeks. The three following verses purport to give a minute description of these seventy weeks, selecting those of their leading events which are of importance in this connection.
Auberlen claimed the 70 years of exile were typical of the 70 weeks, which implies the 70 weeks pertain to the heavenly temple and city rather than the earthly Jerusalem and temples made with hands. And so from the context of the prophecy itself, it is evident that the 70th week spans the whole church age in which Christ confirms his covenant. Yet Auberlen’s concept of the 70th week was chained to the literalistic, preterist notion, that it was limited to seven years. The more enlightened approach to the last half-week frees it from earth-time, and says it is symbolic of the whole age of the church, and so continues to the present day.
1. Karl August Auberlen, Magnus Friedrich Roos: The prophecies of Daniel and the revelations of St John: viewed in their mutual relation, with an exposition of the principal passages. T. & T. Clark, 1856. p. 93.
2. Ibid., p. 93.
3. James Burton Coffman. Commentary on Daniel 9
4. Karl August Auberlen, Magnus Friedrich Roos. Op. Cit., p. 95.
5. Ibid., p. 97.
6. Ibid., p. 97-98.
7. Ibid., p. 98.