Abstract The northwest margin of Junggar basin has abundant hydrocarbon resources, but the geological structure and tectonic evolution are very complicated, with great controversy for a long time. Based on the latest of development exploration and the regional research data, this paper has cleared up the deformation characteristics and the superposed evolution process, as well as explored the relationship between tectonic evolution and hydrocarbon accumulation. The study shows the northwest margin of Junggar basin has the tectonic characteristics of east-west subzone, north-south subsection and vertical stratification. This area experienced five construction phases successively since Permian: Post-orogenic stretch in early Permian, strongly compressional thrust in middle-late Permian, thrust superposed of inheritance in Triassic, oscillating rise and fall overall in Jurassic-Cretaceous as well as the intra continental foreland in Cenozoic. On the whole, this area developed intensive tectonic activities before Triassic and tended to stability after Triassic. There are differences in the processes of tectonic evolution among different area. The three types of vertical superposition of evolution from north to south developed three kinds of complex geological structures. Hashan area belongs to Nappe-Super strip type, Karamay belongs to Overthrust-Super strip type, while Chepaizi area belongs to Thrust-Super strip type. The tectonic evolution and hydrocarbon accumulation have close relationships. Firstly, the different kinds of superimposed evolution determined the types of geological structure, and then controlled different resource, trap, migration pathways and other accumulation elements, as well as the space configuration. Secondly, the multiple tectonic movements resulted many pool-forming periods, and developed many kinds of hydrocarbon accumulation models. The northwest margin of Junggar basin has experienced multi-period of thrust uplift, is a favorable directional zone, the complicated tectonic evolution resulted the characteristics of multiple source for hydrocarbon, multiphase accumulation and three dimensional oil.