The pre-Jurassic in the north depression of the Tuha depression is the most favorable replacement strata to obtain new reserves in the Turpan–Hami Basin. (Pre-Jurassic, in this paper, refers to the Permian and Triassic.) The main source rocks are the Taodonggou Group, of which the burial history and hydrocarbon generation potential remain unconfirmed. The investigation of the burial and thermal history is vital for the basin analysis and hydrocarbon exploration. Therefore, in this paper, by using the acoustic time difference method, vitrinite reflectance method, stratigraphic trend method and PetroMod-1D software, the differential characteristics of denudation thickness, burial history and thermal evolution history of different tectonic units in different periods of Taibei Sag in the Turpan–Hami basin are studied, and their influence on the petroleum system is analyzed, and then the zones with exploration potential are optimized. The results show that the Taibei Sag has experienced multiple tectonic uplift events. The Late Indosinian movement has profound effects on the Taodonggou Group source rocks. The rather large uplift amplitude postpones the maturation of source rocks. In addition, the Turpan–Hami Basin is a typical cold basin. Therefore, the thermal maturity of the source rocks is relatively low, with respect to the relatively deep burial. The thermal histories of the different sub-sags in the study area are slightly differentiated from each other. The Taodonggou Group source rocks in the Taibei Sag generally became mature during the Mid–Late Jurassic epoch, except for those in the Central–Southern Shanbei sub-sag, represented by Well LT-1, which reached the mature stage during the Late Triassic epoch. The study area has well-developed reservoir rocks, and effective reservoir bodies are formed in the slope zone and near the Tainan Sag, due to the higher porosity and permeability of reservoir rocks. The statistics related to the faults and an analysis of the structural styles of oil reservoirs indicate that the structural slope and anticline of the Huobei, Lianbei and Shanbei sub-sags are favorable for increasing reserves and production of hydrocarbons.