Promoting the permeability of deep, low-permeability coal seams through biological means is currently a research hotspot for enhancing the efficiency of coalbed methane extraction. There are few reports in the literature on whether it is possible to promote the development of the microstructure of the coal matrix by the degradation and metabolism of certain groups of functional microorganisms under the stimulation of nitrogen sources. In this study, we selected anthracite coal from Sihe Mine for microbial anaerobic degradation culture experiments. The effects of adding functional microorganisms on the microstructure of anthracite coal under the stimulation of nitrogen source was analyzed by high-throughput sequencing of samples before and after the cultivation and microcharacterization experiments of coal samples. The results showed that the peak amount of residual methane desorption from the coal during the biodegradation process in the experimental group reached 0.640 mL/g coal, and the cumulative amount of methane desorption in the whole period was as high as 1.318 mL/g coal. 16S rRNA high-throughput sequencing results indicated that the bacterial community structure had undergone significant succession after the biodegradation experiments, and that the Firmicutes represented by Bacillus(82.41% of the total) occupied the dominant niche. Metabolic pathway analysis based on KEGG database showed that the degradation of aromatic compounds by microorganisms appeared to be significantly enhanced by the addition of nitrogen sources. Alaso, the relative abundance of a number of key metabolic enzyme genes capable of catalyzing the introduction of oxygen-containing functional groups into the structure of the coal molecule and the de-cyclization reaction were increased. FTIR experiments revealed that biodegradation stimulated by nitrogen source reduced the aromaticity of coal by 59.62% and enhanced the hydroxyl functional group content by 1.822 times.Mercury pressure and low-temperature nitrogen adsorption experiments showed that the micropore pore volume of the treated coal decreased by 34.09%, and the macropore pore volume accounted for an increase of 168.28%, with an average pore size increment of 60.72 nm, and the adsorption level of the gases decreased by 46.1%. Therefore, the nitrogen source can stimulate Firmicutes on the degradation of polycyclic aromatic hydrocarbon and increase the content of oxygen-containing functional groups, which might promote the development of pores in coal and make the difficult-to-desorption methane desorb rapidly.