The Kuqa foreland basin is an important petroliferous basin where gas predominates. The Kela-2 large natural gas reservoir and the Yinan-2, Dabei-1, Tuzi and Dina-11 gas reservoirs have been discovered in the basin up to the present. Natural gases in the Kelasu district and the Yinan district are generated from different source rocks indicated by methane and ethane carbon isotopes. The former is derived from both Jurassic and Triassic source rocks, while the latter is mainly from the Jurassic. Based on its multistage evolution and superposition and the intense tectonic transformation in the basin, the hydrocarbon charging history can be divided into the early and middle Himalayan hydrocarbon accumulation and the late Himalayan redistribution and re-enrichment. The heavier carbon isotope composition and the high natural gas ratio of C1/C1-4 indicate that the accumulated natural gas in the early Himalayan stage is destroyed and the present trapped natural gas was charged mainly in the middle and late Himalayan stages. Comparison and contrast of the oils produced in the Kelasu and Yinan regions indicate the hydrocarbon charging histories in the above two regions are complex and should be characterized by multistage hydrocarbon migration and accumulation.