The development of geochemical exploration technologies unaffected by marsh microorganisms is necessary to improve the prediction of wells and explore for natural gas hydrates in mid-latitude permafrost areas. Here, we examine the potential of inert gas as a new tool for the investigation of gas hydrates in permafrost areas. The study area, 150 km² in size, is situated in the alpine wetland landscape of the Qilian Mountains. The sampling density and depth were 2 points/km² and 60 cm, respectively. In total, 300 soil and headspace gas samples were collected. The chromatographic backflush technique was used to analyze the inert gases helium (He) and neon (Ne) in the headspace gas samples. A comprehensive interpretation was conducted based on geological and geochemical survey results. We propose a geogas migration mechanism of inert gases in the soil above the natural gas hydrate deposits. The inert gas 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. Thus, inert gas anomalies are practical tools for natural gas hydrate exploration in permafrost areas.