Abstract: Junggar Basin is the largest and richest petroliferous basin in the northern Xinjiang area. With the deepening of exploration and more abundant of exploration data, it will provide guidance for the overall exploration deployment by re-studying the formation and distribution of oil and gas reservoirs in the basin, and identifying hydrocarbon enrichment formations of major oil and gas fields. Through the dissection of oil and gas reservoirs, recognition of effective source rocks distribution and the differences of their hydrocarbon generation potential, and combining the petroleum geological conditions and tectonic evolution in the basin, this paper carries out a systematic study on the complexity of hydrocarbon accumulation using seismic data, well data, well testing and oil-source correlation data. The results show that Junggar Basin has experienced multi cycle evolution of carboniferous marine-continental transitional facies and Permian-Cenozoic intracontinental basin. Multiple sets of structural layers, such as the Carboniferous, Middle-Lower Permian, Upper Permian—Triassic, Jurassic, Cretaceous and Cenozoic, are formed. Three sets of main source rocks, including the Carboniferous, Middle-Lower Permian and Middle-Lower Jurassic and three sets of regional caprocks of Middle-Lower Permian, Upper Permian-Triassic and Cretaceous are developed, forming three major petroleum systems of Carboniferous, Permian and Jurassic. The large unconformity surfaces between the top Carboniferous, Middle-Lower Permian, Middle-Lower Jurassic Badaowan-Xishanyao Formation and Jurassic and their overlying strata are identified, which control the distribution of primary oil and gas reservoirs in the three major petroleum systems. The four stages of faults developed from the Late Hercynian to Himalayan form a stereoscopic hydrocarbon transport network in the basin, and connect three petroleum systems vertically, resulting in a complex but orderly distributed oil and gas accumulation system with independent and interrelated primary and secondary oil and gas reservoirs.