The discovered natural gas is mainly composed of middle—small scaled and secondary filled gas fields, accumulated in middle and shallow strata in the Junggar Basin. They can be divided into two accumulation systems of natural gas including lower nearsource original and upper farsource secondary original accumulation system, and the limiting stratum is Baijiantan Formation of Upper Triassic that is territorial mudstone. The former is characterized by abnormal high pressure generally, and the latter has a normal pressure system. By analyzing and comparing accumulation process of natural gas in Eastern Area, Center Area, Northwestern Area and Mosuowan Area, it can be recognized that upper secondary original accumulation of natural gas is from lower original accumulation of natural gas, and the lower strata are more favorable prospect. In addition, the upper accumulation system of natural gas in Southern Area is from coal formation in Jurassic and accumulation of natural gas in lower strata.