In recent years，deep resources in the southern margin of Junggar Basin have been a hot spot for natural gas exploration. Among them，in the middle of the southern margin，the Jurassic source rocks in Huomatu anticline zone have huge potential resources. However，due to the low degree of exploration，the relationship between the thermal evolution of source rocks and the gas accumulation conditions is still unclear. Based on the seismic interpretation and thermal history data，a basin simulation system was applied to restore the thermal evolution histories of Middle and Lower Jurassic source rocks in the southern margin of Junggar Basin.Furthermore，combined with the geochemical characteristics of Jurassic source rocks，the generation and accumulation of gas and the coupling relationships with structural evolution were systematically studied. The research showed that the Middle and Lower Jurassic source rocks developed in the middle of the southern margin. Moreover，the gas mainly generated in the early stage of the Early Cretaceous Epoch（99.6 Ma）and the late stage of the Late Cretaceous Epoch（65.5 Ma），respectively. Now，the Middle and Lower Jurassic source rocks are in the stage of high and over maturity and still have hydrocarbon generation potential. At the same time，two hydrocarbon accumulation models have been formed in the area，and they are secondary accumulation with late uplift and high-mature accumulation with continuous buried depth. In addition，the gas distribution has been controlled by the evolution of the source rocks and the structure.