Natural gas is a vital energy resource. The isotopic composition of natural gas plays a critical role in understanding its origin, thermal maturity, and secondary alteration. Both kinetic and equilibrium isotopic fractionations have been observed in various natural gas systems. However, the dominant mechanism (either equilibrium or kinetic) that controls the isotopic compositions of the primary natural gas is still unclear. Coalbed gas (CBG), formed and stored in situ coalbeds, is an ideal natural gas for studying this key issue. We collected CBG and coproduced water samples from the Zhuzang syncline in China. This study shows that the CBG is an over-mature thermogenic gas formed during the Yanshanian orogeny. The CH ₄-C ₂H ₆-CO ₂ system was likely near carbon isotope equilibrium during the CBG formation. However, later alterations, such as meteoric water recharge, CO ₂ dissolution, and CBG recovery led to obvious isotopic disequilibrium of the CH ₄-C ₂H ₆-CO ₂-DIC (dissolved inorganic carbon) system. Carbon isotope reversals (δ ¹³C _CH4 > δ ¹³C _C2H6) were observed in the CBG samples, resulting from decreasing δ ¹³C _C2H6 values after CBG formation. Based on isotopic equilibrium, the δ ¹³C values of the primary ethane were estimated. Some hypotheses often used to explain isotope reversals in natural gas cannot explain the isotope reversals of the CBG samples. We propose that the CBG recovery process led to more negative δ ¹³C _C2H6 and thus δ ¹³C _CH4 > δ ¹³C _C2H6. Model-estimated 53–99 % CO ₂ generated during thermogenic or microbial CBG formation has dissolved into coalbed water to become DIC. Hence, dissolution trapping is an important mechanism for CO ₂ storage in coalbeds over geological timescales. This study implies that isotopic equilibrium fractionation plays a vital role in understanding the primary geochemical composition and secondary alteration of CBG.