Natural gas resources in the Qaidam Basin are abundant and of various types. On the basis of the natural gas carbon isotope distribution characteristics, the western Qaidam Basin mainly comprises oil-type gas, whereas the northern margin of the basin primarily contains coal-type gas. These types are of thermal origin. Thermogenic natural gas has the same characteristics in terms of distribution regularities and main controlling factors of reservoir accumulation. In this study, geochemical, geophysical, geological, and basin simulations were comprehensively completed to investigate the thermogenic gas distribution and the main controlling factors of its accumulation in the Qaidam Basin. The distribution of oil and gas accumulation zones based on source rock maturity maps indicates that the oil is distributed in and near low-maturity to mature (0.5% < Ro < 0.8%) source rock areas. Meanwhile, natural gas is distributed in mature (0.8% < Ro < 1.3%) to highly mature (Ro > 1.3%) source rock areas. The areas wherein oil and gas coexist are near and in mature (0.8% < Ro < 1.3%) source rock areas. Thus, the tectonic evolutionary history, paleostructural map, source-reservoir-cap assemblage, and gas accumulation model were analyzed. The results indicated that the main controlling factors for natural gas reservoir formation are as follows: mature source rocks control the horizontal distribution of natural gas, ancient uplifts or slopes control natural gas migration direction, faults and an unconformity control gas migration channels, and high-quality reservoirs regulate the reserve scale. Moreover, locating favorable reservoirs can be the subsequent step in natural gas exploration near and in mature to highly mature source rock areas along paleouplifts and ancient slopes with deep faults. Therefore, this study is significant when conducting natural gas exploration in this area.