The hydrocarbon isotope geochemistry of coalbed methane is determined by fractionation during its generation, migration, and accumulation. The isotope can be used to identify the origin type and also provide a basis for the selection of favorable blocks for coalbed methane exploration and development. In this paper, the anaerobic fermentation of coal was conducted to generate primary biogenic gases. The carbon and hydrogen isotopes, liquid organic compounds, and microbial communities were analyzed using isotopic mass spectrometry, gas chromatography–mass spectrometry, and high-throughput sequencing methods. The results show that acetolactic methane was generated first and had the lowest carbon isotope; methylotrophic methane was produced in the early-middle stage and had moderate carbon isotope; and hydrotropic methane was generated at the middle-late stage and featured a broader carbon isotope distribution. The production of methane differs significantly between carbon and hydrogen isotopes produced in the laboratory and those of natural methane. This is caused by a series of fractionations induced by dissolution, adsorption, desorption, and diffusion of microbial methane during migration and accumulation.