Abstract: Based on the theory of superimposed deformation and the regional tectonic background, the multi-phase non-coaxial superimposed structures in Junggar Basin were systematically analyzed using seismic interpretation, field outcrop observation, and paleo-stress field recovery methods according to the characteristics of the current tectonic framework. Moreover, the tectonic evolution process of the basin was reconstructed using sandbox analogue modelling technology. The results showed that the study area has experienced five phases of non-coaxial deformation with superimposition: The first phase of deformation (D1) is characterized by NNE-SSW extension during late Carboniferous to early Permian, which formed large graben, half graben and other extensional structure style around the basin. The second phase of deformation (D2) is represented by NE-SW compression during the middle to late Permian, and it comprised numerous contraction structures that developed based on D1. The basic form of the entire basin is alternating uplift and depression. The third phase of deformation (D3) is the NW-SE transpressional strike-slip in the Triassic-Jurassic, which produced numerous strike-slip structural styles in the middle part of the basin. The fourth phase of deformation (D4) is the uniform sedimentation during Cretaceous, and the fifth phase (D5) is the compression along NNE-SSW due to the North Tianshan northward thrust, which produced three rows of fold thrust belts and tear faults in the front of the mountain in the southern margin of the basin. The newly established three-dimensional tectonic evolution model shows that, based on the large number of NW-trending grabens and half grabens in the Carboniferous basement of Junggar Basin, multiple level NE trending uplifts have formed with the joint superposition of the late structural inversion and multiple stress fields. This has resulted in the current tectonic units of alternating uplifts and depressions in different directions in the study area.