Abstract: To explore the microstructural evolution mechanisms of low-rank lignite (Coal A) and bituminous coal (Coal B) during microbial anaerobic fermentation. Coal samples from Hulunbuir (Inner Mongolia, Coal A) and Changji (Xinjiang, Coal B) were subjected to anaerobic fermentation with microorganisms. The physicochemical properties of coals at different fermentation stages were analyzed using low-temperature liquid nitrogen adsorption, X-ray diffraction (XRD), nuclear magnetic resonance (NMR), and X-ray photoelectron spectroscopy (XPS). Molecular mechanics, molecular dynamics, and adsorption theories were integrated to investigate the response of coal molecular structures to microbial degradation. The results indicate that: Methane production showed a positive correlation with the most probable pore diameter (R²=0.874) and full width at half maximum (R²=0.910), but a negative correlation with aromatic layer extension (R²=0.915), indicating that reduced structural order promotes methane generation. Both coals exhibited mesopore-dominated structures. The specific surface area decreased initially, then increased, and finally declined. Microbial metabolites altered pore structures, increasing micropores and mesopores, thereby enhancing methane adsorption. Molecular structural changes included cleavage of aliphatic side chains, degradation of oxygen-containing functional groups (e.g., carboxyl and hydroxyl), and disruption of aromatic structures. Coal A’s oxygen-rich functional groups accelerated degradation, while Coal B’s condensed aromatic layers slowed degradation due to π—π interactions. Coal B’s high aromaticity and ordered stacking via van der Waals forces strengthened methane adsorption through π—π interactions. In contrast, Coal A’s loose structure weakened adsorption capacity. Prolonged microbial action redistributed adsorption sites in Coal A uniformly, whereas Coal B showed minimal adsorption reduction. Microbial degradation significantly enhances volatile organic compound production through cumulative effects. Future studies should focus on microbial-coal interaction mechanisms, enzymatic pathways, and degradation kinetics to comprehensively elucidate structural modifications at the microscale.