Understanding the bioconversion process of lignite to methane is an important contribution to the establishment of effective utilization of the existing coal resources and the acquisition of environmental biofuels. Microorganisms from coal seams were acclimatized using lignite as the sole carbon source to improve the bioavailability of coal. The contribution of acclimation to biomethanation was discussed from the aspects of mathematical models, the changes of key intermediates in the liquid phase, and the dynamic evolution of the community structure. The results showed that the anaerobic digestion (AD) efficiency of lignite was significantly improved after acclimation. The methane yield revealed that the methane-producing capacity of the bacteria and the bioavailability of lignite were enhanced. The data of 16S rDNA also suggested that the diversity of the bacterial and archaeal communities increased significantly. The stability of the AD system was enhanced. The abundance and types of bacterial genera that had a symbiosis with methanogens increased. The gene function abundance and the reading number of the bacteria in terms of membrane transport, cell motility, and xenobiotic biodegradation and metabolism were significantly improved with acclimation. This study provides an experimental basis for microbially enhancing coalbed methane (MECBM) and clean energy production.