Early microbial gas has been sealed in reservoirs in the Miquan region of NW China, with little or no supply of current microbial gas. To date, the environmental conditions and mechanisms restricting microbial methanogenesis are still unclear in the Miquan region. Thus, in this study, a series of gas and water samples from coalbed methane (CBM) exploitation wells and in situ coal samples were collected and analyzed to determine the potential for current microbial gas generation, the methanogenic pathways, the source of nutrients, the influence of the environmental conditions on in situ microbial communities and their methanogenesis, and the mechanisms restricting microbial methanogenesis. The gas-production simulation experiments revealed that the existing microbes in the coalbed water were less efficient at converting coal into methane under the approximate in situ conditions, which further verified that there was little or no supply of current microbial gas. The stable isotope compositions of the gas samples suggested that carbon dioxide (CO2) reduction was the dominant metabolic pathway for generating CBM, whereas the methanogenic communities contained a mixture of acetoclastic and methylotrophic methanogens in local areas. The nutrients available for the microbes mainly included the total dissolved nitrogen (TDN) and total dissolved carbon (TDOC), and the in situ dissolution of the coals was a significant source of the TDN, whereas the TDOC was mainly supplied by surface water. The microbes in the different tectonic settings were significantly controlled by different combinations of environmental factors, and there was no single environmental factor that completely dominated the spatial variability of the microbial communities. The gradual stagnation of the water environment led to an increase in salinity and a decrease in nutrients, which were likely the main factors restricting microbial methanogenesis under in situ conditions. Combined with the results of the rate-limiting stages of the anaerobic fermentation, the mechanisms restricting microbial methanogenesis can be finally determined in the Miquan region. These discoveries presented in this case study provide a significant supplement to the geological theory of CBM accumulation, and have a guiding significance for CBM development in the Miquan region.