Abstract: Using the data of seismic, surface outcrop, drilling, logging and non-seismic geophysics, the paper investigates the basin structure, tectonic style and regional tectonic evolution of Mesozoic strata in Kuqa depression, Tarim basin. Stratum trend thickness method is adopted to calculate the Mesozoic denudation thickness and the genesis of the Mesozoic prototype basin is analyzed in Kuqa depression with sedimentary data. The residual Mesozoic strata in Kuqa depression are generally of a geologic framework characterized by thick in the north and thin in the south, denudating in the north and overlapping in the south, strong angular unconformity developed on the Hercynian fold belt of the southern Tianshan Mountain in the north and slight angular unconformity distributed on the Cambrian-Ordovician series. The Mesozoic prototype basin in Kuqa depression is a down-wrapped basin overlying the Hercynian orogenic belt of the southern Tianshan Mountain and the transitional zone at the margin of Tarim craton. The isostasy may provide the main force for the subsidence of the basin. The Hercynian movement resulted in the uplift of the southern Tianshan folds. Strong volcanism occurred in Tarim craton and southern Tianshan Mountain during the early Permian allowed the formation of proto-Kuqa depression basin on the basin-mountain transitional zone. The balanced subsidence of the earthcrust started in Triassic period, the orogenic belt collapsed and the depression basin was developed on the basin-mountain transitional zone. The successive development of the depression occured in Jurassic and Cretaceous, but the basin axis, sedimentation and depositional center slightly migrated and the regional uplift-denudation occurred in the Late Cretaceous