Microorganisms play vital roles in the biogeochemical processes, such as biomethane production, which is an important source of coal bed methane (CBM), that occur in coal beds. However, little information is available regarding the microbial communities in in situ coal beds of different ranks from Permian mining areas. In this study, anaerobic Biolog ECO microplates were used to determine the microbial metabolic activity, and high-throughput sequencing was used to investigate the bacteria and archaea communities in three typical mining areas. Anaerobic Biolog ECO microplates showed that the peak value of average well color development (AWCD) in low-rank coal seams from Anhui Province (A-L) was 0.46 higher than that of medium-rank coal from Shanxi Province (S-M). Phylogenetic analysis indicated that the bacterial phyla Proteobacteria, Firmicutes, and Actinobacteria were the predominant lineages in all samples, in particular, the family Oxalobacteraceae accounted for the overwhelming majority of the bacterial sequences (from 47.20 to 92.67%). Most of the identified genera, Herbaspirillum, Pseudomonas, and Acinetobacter, were fermentative bacteria that can convert coal macromolecules into methanol, acetic acid, and CO2. In addition, the archaea in A-L were dominated by the phyla Euryarchaeota, Thaumarchaeota, and Woesearchaeota. Additionally, Euryarchaeota was the dominant archaeal lineage in S-M, and Thaumarchaeota was predominant in the Guizhou Province group of high-rank coals (G-H). Canonical correspondence analysis (CCA) showed that there were significant correlations between the microbial community and porosity, hydrogen content, and oxygen content (p < 0.05). The KEGG pathway analysis indicated that biomethane production mainly depended on archaea and that the methane metabolism capacity of A-L coals was the highest. Overall, the results suggest that the diversities of the microbial communities were related to the porosity and chemical elements of the different ranks of coal.