Geological mapping, interpreted cross sections, structural analyses and residual thickness maps were used to characterize the evolution of stress setting, structure and stratigraphic distribution of the Chepaizi Uplift, which is a NW-SE trending structure located in the Western Junggar Basin. The NS-trending faults show an important transpressional phase during the Late Permian, as demonstrated by tectonic stress field and stratigraphic thickness variations. A major compressional thrusting and strike-slip phase during the Late Jurassic created a series of NW-SE faults that originated by the large-scale uplift event in the Northern Tianshan. Faults were reactivated as thrust and dextral strike-slip faults. In addition, the angular unconformity observed between Jurassic and Cretaceous provide evidence of this tectonic event. Lots of normal faults indicate that the area records southward tilting and regional derived extensional stress that took place during the Neogene. Before that, thick Early Cenozoic strata are widely deposited. The balanced cross-section highlights the evolution of stress setting and stratigraphic distribution of the Chepaizi Uplift.