The Paleogene and Neogene oil and gas in the western Qaidam basin have a regular distribution in three concentric zones from the edge to the center of the basin. Natural gas mainly occurs in the inner zone, and the gas-oil ratio of the northern area of the basin is significantly higher than that of the southern area. Large amounts of carbon isotope data of natural gas, plotted in X-shaped and comprehensive identification diagrams for the southern area and northern area, respectively, were used to identify the types of natural gas. The large-scale distribution of natural gas is highly consistent with the Ro values of major source rocks, but is poorly correlated with the type of organic matter. This indicates that the main controlling factor of natural gas distribution is organic matter maturity, and the kerogen types act as the basis for the formation of different types of natural gas. Paleouplifts and squeezed anticlines near hydrocarbon generation depression centers, which are major natural gas-rich regions, control the migration directions of natural gas, while hydrocarbon migration pathways and fault systems connecting gas sources are the most important factors for natural gas reservoir formation in the inner basin. Therefore, favorable zones for natural gas distribution can be predicted on the basis of the distribution of thermal evolution and the gas generation intensity of major source rocks as well as the structural map. The Shizigou-Youshashan-Yingdong-Dawusi, Youquanzi –Kaitemilike - Youdunzi, and Xiaoliangshan – Nanyishan - Dafengshan structural belts are favorable zones for natural gas accumulation. This study has important theoretical and practical significance for future natural gas exploration.