The Kuqa depression, located at the northern edge of the Tarim basin, is filled with extremely thick Mesozoic clastic sedimentary strata, with a maximum residual thickness exceeding 6000 m. The mudstone and coal- bearing rocks contained in the Triassic and Jurassic formations are considered the primary hydrocarbon source rocks in the depression. Due to the complex surface conditions and underground tectonic deformation, the distribution of the Mesozoic strata in the Kuqa depression revealed by seismic data is not clear. This led to significant differences in understanding the characteristics of the Mesozoic prototype basin. Recent interpretations of extensive 3D seismic datasets acquired across the Kuqa depression have identified a large number of deep- seated normal faults in the lower Mesozoic strata. These faults control the distribution of sedimentary thickness in the Triassic and even the Lower Jurassic. The discovery of these deep normal faults, which controlled the early Mesozoic sedimentation, indicates that the early Mesozoic Kuqa depression basin should be an extensional or strike- slip extensional fault- controlled basin. This paper, based on the results of 3D seismic data interpretation, analyzes the structure of the Mesozoic basin in the Kuqa depression and its subsequent tectonic evolution. The results show that the late Mesozoic basin was an extensional basin superimposed on the Hercynian orogenic wedge of the southern Tianshan. Under the influence of late Mesozoic and Cenozoic regional compressions and the uplift of the new Tianshan, the early Mesozoic normal faults were reconstructed or inversed to different degrees, resulting in the formation of complex contractional structural deformation. The Mesozoic source rocks in some areas became the local detachment layer of late thrust fold deformation, while others were overthrust to become the “dead zone” under the detachment fault in the deeper fault depression. This new structural interpretation model for the Early Mesozoic basin not only explains the variations in oil and gas accumulation zones and subdivisions within the Kuqa depression but also provides valuable insights for deep oil and gas exploration and identifies key geological problems requiring further study. The existence of Triassic and Jurassic source rocks located in the “dead zone” footwalls of inversed faults (including detachment faults) in the Kuqa depression provides a crucial material basis for deep oil and gas accumulation.