Jurassic coal and carbonaceous mudstone collected from the Turpan-Hami Basin were pyrolysed in a closed system using a microscale sealed vessel (MSSV). The stable carbon isotope composition of methane, ethane and propane of pyrolysis gases were analysed and compared with the natural gases in the basin to identify their origin and post-genetic alteration. Similar origins of ethane and propane between pyrolysis gases and natural gases were observed in our studies. However, the methane of the natural gases experienced post-genetic alteration. Gases from Well Tuocan-1 of the Yilahu oil field and a number of wells in the Baka oil/gas field are the results of the admixture of oil-associated gas and coal-derived gas and of bio-degradation of coal-derived gas, respectively. The gas pools likely exist in volcanic rock below the Jurassic strata within the Turpan-Hami Basin, which was inferred from geochemical and geological evidence. Consequently, most of the natural gases in the Turpan-Hami Basin were probably the mixtures of matured coal-derived gases and the methane which diffused upward from gas pools at greater depth.