Based on the organic geochemical data and the molecular and stable carbon isotopic compositions of natural gas of the Lower Permian Fengcheng Formation in the western Central Depression of Junggar Basin, combined with sedimentary environment analysis and hydrocarbon-generating simulation, the gas-generating potential of the Fengcheng source rock is evaluated, the distribution of large-scale effective source kitchen is described, the genetic types of natural gas are clarified, and four types of favorable exploration targets are selected. The results show that: (1) The Fengcheng Formation is a set of oil-prone source rocks, and the retained liquid hydrocarbon is conducive to late cracking into gas, with characteristics of high gas-generating potential and late accumulation; (2) The maximum thickness of Fengcheng source rock reaches 900 m. The source rock has entered the main gas-generating stage in Penyijingxi and Shawan sags, and the area with gas-generating intensity greater than 20×108 m3/km2 is approximately 6 500 km2. (3) Around the western Central Depression, highly mature oil-type gas with light carbon isotope composition was identified to be derived from the Fengcheng source rocks mainly, while the rest was coal-derived gas from the Carboniferous source rock; (4) Four types of favorable exploration targets with exploration potential were developed in the western Central Depression which are structural traps neighboring to the source, stratigraphic traps neighboring to the source, shale-gas type within the source, and structural traps within the source. Great attention should be paid to these targets.