Through the east and west orogenic geological cross-section observation sides of Junggar Basin, the system fission track dating and thermal analysis of the evolution of simulation results, combined with previous research findings, the Junggar Basin in the peripheral orogenic belt, mainly through the late Mesozoic tectono-thermal event. Through fission-track analysis and comparison，Orogenic belts on both sides of the Junggar Basin has a different Uplift history.The northwestern margin of the Junggar basin as early as in the eastern part of the uplift, the uplift rate is greater than the eastern part of. Northwestern margin of Junggar Basin has experienced since the Cretaceous period from the edge of the Junggar Basin to the Zaire mountain uplift events followed one after another, indicating that the northwestern margin of the Junggar thrust fault system thrust to the internal basin by overstep propagation. Junggar Basin, east-west belt of rocks on both sides of fission track data are a reflection of the cooling since the Cretaceous uplift events, and fully confirmed by the late Yanshan tectonic movement prevalent in the Junggar region, which provide vital evidence for a detailed study Yanshanian intracontinental tectonic activities in northern Xinjiang.