The development of geochemical exploration technologies unaffected by marsh microorganisms isone of the important issues to improve the prediction and exploration for natural gas hydrates in mid- latitude permafrost areas. The potential of inert gases as a new tool for the investigation of gas hydrates in permafrost areas using He and Ne test methods was investigated in this paper. The study area with a size of 150 km2 is located in the alpinearctic swamp landscape of the Qilian Mountains. The sampling density and depth are 2 points/km2 and 60 cm, respectively. In total, 300 headspace gas samples and 400 core samples were collected and the chromatographic backflush technique was used to analyze the inert gases (helium and neon) in the headspace gas samples. Combined with the comprehensive interpretation of geological and geochemical exploration, our study indicates that the anomalies of inert gases have close relationship to natural gas hydrate reservoir, and are within the range of hydrocarbon anomalous concentration, suggesting an atop anomalous mode. Ten of the 11 gas hydrate wells discovered in the experimental area of Juhugeng are located within the anomalious area of He and Ne; only one well is outside of the anomalous area. This study analyzed the vertical distribution pattern of light hydrocarbon, helium, and neon in the headspace gas of hydrate drilling. We propose a geogas migration mechanism of inert gases in the soil above the natural gas hydrate deposits. The He and Ne anomalies near the ground surface of the Muli coalfield in the Qilian Mountains, derived from the deep hydrate deposits and fault structure, are not affected by marsh microorganisms; they are the effective tools for natural gas hydrate exploration in permafrost areas.