Studies on gas isotopes of natural gas hydrates recovered from the Qilian Mountains permafrost is an effective way to understand the genesis and origin of the gas. In this paper, 8 gas hydrate bearing core samples have been collected from 2 scientific drilling holes (DK2 and DK3 ) at the southern foot of the Qilian Mountains permafrost. The results indicate that the hydrate-hound gases in the Qilian Mountains permafrost are mainly thermogenetic gas originating from organic genetic gas formed in a freshwater environment.