Methane is an economic energy resource and potent greenhouse gas. Distinguishing secondary microbial methane from thermogenic gas is important for natural gas exploration and consideration of subsurface microbial activity in the global carbon cycle, but remains challenging. To understand controls on methane origins in natural gas systems, we investigated the methane clumped isotopologue distributions in the Qinshui Basin high-thermal maturity coal bed methane (CBM) reservoir. Here, near-equilibrium clumped isotopologues distribution (Δ13CH3D and Δ12CH2D2) inferred a temperature interval of 21.6–252.3 °C. The high-temperature thermodynamic equilibrium most likely represents original thermogenic CBM characteristics during coalification. The low-temperature equilibrium clumped isotopologue distributions suggest microbial alteration to CH4 isotopic bond ordering by increased enzymatically catalyzed isotopic exchange. The independent constraints from clumped isotopes, integrated with other geochemical and genomic evidence, confirm notable secondary microbial methane from biodegradation in the highly mature reservoir. Thus, methane clumped isotopes can be used as unequivocal tracers to distinguish secondary microbial methane from thermogenic gases and hence provide the ability to incorporate them separately into global methane budgets.