Secondary microbial gas accompanied by abnormally high CO2/N2 concentrations is widely developed in the southern Junggar Basin (SJB). However, the mechanism of nonhydrocarbon-enriched coalbed methane (CBM) remains unclear. Due to the close correlation between microbial gas and hydrogeology, the geochemical and microbial sequencing experiments were conducted to reveal hydrogeological controls on CBM geochemistry in this study. The results showed that CBM derives from thermogenic and biogenic genesis in SJB, and the biogenic genesis is mainly generated through CO2 reduction. CO2 is biogenic and N2 is of atmospheric and thermal genesis. CO2 concentration mainly depends on microbial production and consumption. The higher alkane-degrading bacterial abundance in As/V-enriched environments promotes CO2 generation, while high HCO3− contents inhibit CO2 dissolution in water and consumption by methanogens. Alkane-degrading bacteria enrichment and discontinuous CO2 consumption lead to the significantly high CO2 concentration. Atmospheric N2 concentration was negatively correlated with groundwater runoff intensity, while thermogenic N2 concentration showed a weak correlation with total dissolved solids (TDS). High atmospheric infiltration and thermogenic N2 replenishment lead to a N2 concentration exceeding 10%. Stable carbon isotopes are related to methanogens, and more methanogens in Li/Zn/Cu/Rb/Sn-enriched environments lead to decreasing δ13C–CH4. However, when TDS exceeds 15,000 mg/l, the inhibited methanogen production results in δ13C–CH4 higher than −55‰. Three CBM geochemistry distribution models were ultimately established: atmospheric mixed in the runoff–weak runoff area, reformation by shallow microbial gas migration in the weak runoff–stagnant area, and damping microbial gas generation with abundant alkane-degrading bacteria in the weak runoff–stagnant area.
