Both of the Hala Lake Depression in Qilian Mountain and the Muli Depression in which natural gas hydrate was found are depressions of the South Qilian Basin and have similar hydrate accumulation conditions. However, due to the low degree of geological work in the Hala Lake Depression, the geological structure information in the depression under the Quaternary overburden is unclear, and the gas hydrate accumulation conditions in this area are not well understood. In order to find out the geological structure characteristics and gas hydrate accumulation conditions of the Hala Lake Depression, the authors carried out a comprehensive study of geophysical and geochemical exploration in the depression. Some conclusions have been reached:(1) The investigation area can be divided into four sags, two salients and twenty-six faults; (2) As for the distribution characteristics of permafrost layers in the investigation area, the Cenozoic sedimentary areas are mainly in sheet distribution in large area and the outcrops of bedrock are mainly in island-shaped distribution; the development of the permafrost layer is closely related to factors such as elevation, topography, land cover and surface soil moisture; (3) Two geochemical anomalies were found in the investigation area, and the indicators combination of heavy hydrocarbon in acidolysis hydrocarbons, aridity coefficient of acidolysis hydrocarbons, methane in headspace gases and fluorescence spectra characteristics indicates that there are two different types of anomalous features characterized by an obvious anomalous concentration center with relatively high intensity; (4) The source rocks in the Hala Lake Depression are relatively poor, and the preservation integrity of source rocks and the Indosinian-Yanshanian trap structure are the key factors to hydrate accumulation. The northern part of the Hala Lake Depression and the No. I geochemical anomaly zone can be the prospective areas for hydrate accumulation, and these findings provide a basis for future investigation and evaluation of the gas hydrate resources in the South Qilian Basin.