Abstract: Microbial degradation is one of the effective methods to improve the permeability of low-permeability coal and enhance gas extraction efficiency. Clarifying the mechanism of molecular structure changes in coal under microbial degradation has theoretical significance for coal reservoir transformation. In order to explore the changes in molecular structure during coal biodegradation, a simulation experiment of microbial anaerobic degradation of three different degrees of coal (bituminous coal, anthracite coal, and coking coal) was conducted under laboratory conditions. Industrial/elemental analysis, infrared spectroscopy (FTIR), X-ray diffraction (XRD), liquid chromatography-mass spectrometry (LC-MS), and high-throughput sequencing of 16S rRNA were used to characterize the functional groups, crystal structure, and metabolic products on the coal surface before and after microbial degradation. The molecular structure changes and mechanisms of coal with different degrees of metamorphism under microbial degradation were also explored. The results indicate that the biodegradation of coal is a process of enriching carbon elements (increasing C element by 1.28%−4.04%) and removing hydrogen, oxygen, nitrogen, and sulfur elements. Biodegradation destroys the ether bond (C—O—C) and carbonyl (C=O) structures, causing the aliphatic side chains of coal to break and surface functional groups to detach. This degradation behavior results in the presence of organic heterocyclic compounds, organic oxygen compounds, organic acids and their derivatives, benzene, lipids, and lipid molecule metabolites in the culture medium. In addition, biodegradation breaks the weak bridging bonds between aromatic layers in coal, leading to the cracking of polycyclic aromatic hydrocarbon structures and an increase in aliphatic side chains, resulting in a slight improvement in the aromaticity of coal samples. These results indicate that biodegradation promotes an increase in the aromaticity and maturity of coal, altering the degree of condensation of coal aromatic rings, similar to the peatification process of coal. The differential degradation mechanisms of coal with different degrees of metamorphism by microorganisms deserve further in-depth research.