Helium is a critical, strategic and nonrenewable resource with limited reserves and unstable supplies. However, the helium sources and migration processes in petroliferous basins remain unclear. The Qaidam Basin features multiple reservoir layers, multiple genetic types of natural gas, and varying helium concentrations, providing an ideal natural laboratory for understanding the helium enrichment processes. Here, we present the original noble gas isotopic compositions and major gas components of 11 microbial gas samples from three gas layers in the Sebei No.1 gas field, eastern Qaidam Basin, China. The helium isotopic ratios range from 0.007 to 0.057 Ra, reflecting a predominantly crustal source. The Quaternary Sebei microbial gas features much lower helium concentration (0.0003–0.001%), 21Ne/22Ne ratio (0.031–0.034), and 40Ar/36Ar ratio (292–380) than thermogenic natural gases in the Qaidam Basin. The middle gas layer (II) of the Sebei gas field features higher 21Ne/22Ne and 40Ar/36Ar ratios than the top and bottom gas layers, displaying positive correlations with higher 4He groundwater concentrations before degassing, as calculated from 4He/20Ne ratios and 20Ne concentrations in air-saturated water. However, the correlations between the 4He contents in natural gas and the 21Ne/22Ne and 40Ar/36Ar ratios are unclear, suggesting that 4He dissolves into the groundwater system before degassing into a gas reservoir and that the variations in the 4He concentration in the gas phase are caused by the different levels of hydrocarbon dilution. Quantitative calculations of helium production revealed an external helium flux from the crustal basement except for the in-situ production from sedimentary strata even in this broadly-defined self-generating and self-preserving natural gas system. The helium resources in the Qaidam Basin are mainly distributed in tectonically active zones with uplifted pre-Jurassic basement rocks (providing sufficient helium sources), ancient groundwater systems (accumulating more helium) and suitable hydrocarbon production (acting as a carrier gas but diluting helium as slightly as possible).