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Natural gas hydrate, oil and gas were all found together in the Qilian Mountain permafrost area, northeast of Qinghai-Tibet Plateau, China. They are closely associated with each other in space, but whether they are in any genetic relations are unknown yet. In this paper, a hydrocarbon gas-generation series, gas-fluid migration series and hydrocarbon gas-accumulation series are analyzed to probe the spatial, temporal and genetic relationships among natural natural gas hydrate, oil and gas. The subsequent results show that natural gas hydrate, oil and gas actually form a natural gas hydrate-oil-gas system. Based on the Middle Jurassic and the Upper Triassic hydrocarbon gas-generation series, it is divided into four major sub-systems in the study area: (1) A conventional Upper Triassic gas-bearing sub-system with peak hydrocarbon gas-generation in the late Middle Jurassic; (2) a conventional Middle Jurassic oil-bearing sub-system with low to mature hydrocarbon gas-generation in the late Middle Jurassic;(3) a natural gas hydrate sub-system with main gas source from the Upper Triassic gas-bearing sub-system and minor gas source from the Middle Jurassic oil-bearing sub-system as well as little gas source from the Middle Jurassic coal-bed gas and the microbial gas;(4) a shallower gas sub-system with microbial alteration of the main gas source from the Upper Triassic gas-bearing sub-system. This natural gas hydrate-oil-gas system and its sub-systems are not only theoretical but also practical, and thus they will play an important role in the further exploration of natural gas hydrate, oil and gas, even other energy resources in the study area.