Based on the pyrolysis products for the Jurassic low-mature coal under programmed temperature, and chemical and carbon isotopic compositions of natural gas from the Kuqa Depression, the genetic origin of natural gas was determined, and then a gas filling model was established, in combination with the geological background of the Kuqa Depression. The active energy of CH4, C2H6 and C3H8 was gotten after the data of pyrolysis gas products under different heating rates (2°C/h and 20°C/h) were fitted by the Gas Oil Ratio (GOR) Isotope Model soft. When the frequency factor (Af) was chosen as 1×1014, the active energy of CH4, C2H6 and C3H8 was 58?kcal/mol, 57?kcal/mol and 54?kcal/mol, respectively. The distributive ranges of the δ13C1,? δ13C2 and δ13C3 values for the pyrolysis gas products are –35.9‰ to –30.7‰, ?26.2‰ to ?21.3‰ and ?26.4‰ to ?22.7‰, respectively. All of the natural gases from the Kuqa Depression are dominated by hydrocarbon gases, with the high gas dryness (C1/C1?4) at the middle and northern parts of the depression and the low values at both east and west sides and the southern part. The carbon isotopes of methane and its homologs as a typical coal-type gas are enriched in 13C, and the distributive range of the δ13C1,? δ13C2 and ?δ13C3 value is ?32‰ to ?38‰, ?22‰ to ?24‰ and ?20‰ to ?22‰, respectively, with the carbon isotopes of gaseous alkanes being less negative with the carbon number. With the ethane being enriched in 13C the increasing tendency of the geological reserve of natural gas in the Kuqa Depression is observed. This observed change is consistent with the results of pyrolysate gas yield of coal as a potential gas source in the Kuqa Depression, suggesting natural gas was thermally derived from the humic organic matters and the carbon isotopes of gaseous alkanes would coarsely predict the geological reserve of gas in the Kuqa Depression. Through the simulation of kinetic processes of gas generation for the Jurassic coal in the Kuqa Depression, the gas in the Kela 2 gas field would get the threshold of gas expulsion after 27?Ma, be expelled out of source rocks as “pulse action”, and then filled in the gas reservoir. The peak gas-filling history took place during the past 2 Ma.