Abstract: Based on an analysis of hydrocarbon gas components and carbon isotopes of methane and ethane at different depths in headspace gases from the core in well DK-9 in Qilian Mountain permafrost, this paper discusses the spatial relationship of the variation of core headspace gas content with gas hydrate and its anomalous sections, oil-gas showing sections, and fault or fracture zones, and indicated the origin of the hydrocarbon in headspace gases. The results show that the sections of 180.26~308.50m, 356.45~399.32m, 458.55~508.65m with gas component content anomalies are comparable with gas hydrate and its major anomalous layer as well as oil and gas showing layer; the anomalous section can be used as an indication of gas hydrate and its major anomalies and oil and gas shows. The relationship between variation of hydrocarbon gas content in headspace gases and the location of fault or fracture zones suggests that different levels of the fault system from the depth can provide a channel for deep hydrocarbon gas migration or the space for the formation of gas hydrate. Methane and ethane carbon isotopes suggest that the hydrocarbon gas in headspace gases is genetically mainly composed of pyrolysis gas, with the mixture of some hybrid genetic gas and biogenetic gas.