Objective: Traditional methods for the prevention of spontaneous coal combustion rely on chemical additives. However, these methods are often costly and potentially polluting. Microbial technology has been gradually applied to the prevention and control of spontaneous coal combustion due to its environmental protection and high efficiency. This study aimed to explore a green and efficient method for inhibiting spontaneous coal combustion through the influence of microorganisms on the microcrystalline structure and oxidation characteristics of lignite and provide new ideas for the diversification and greening of spontaneous coal combustion prevention strategies. Methods: The inhibitory effect of microorganisms on spontaneous coal combustion was analyzed from two aspects: microstructure and macroscopic oxidation characteristics. In the experiment, lignite samples from a coal mine in Inner Mongolia were used, and Sphingomonas polyaromaticivorans was selected for the bacterium-coal mixing experiment. X-ray diffractometer and Fourier transform infrared spectroscopy experiments were used to analyze the microstructural changes in lignite after microbial treatment. Moreover, alterations in the minerals and functional groups in the coal were revealed to gain insights into the effects of microbial treatment on coal microstructure. In addition, the key thermodynamic parameters, such as characteristic temperature, thermal weight loss, and thermal loss rate of coal samples in the oxidation and spontaneous combustion process, were analyzed through macroscopic thermal analysis techniques, such as thermogravimetric analysis (TGA) and differential scanning calorimetry. Results: The experimental results show the following: (1) The microcrystalline structure of the coal sample tended to be orderly and graphitized after microbial treatment, and the average crystallite diameter and the number of effective stacked aromatic flakes were considerably reduced by 32.04% and 27.22%, respectively. These results indicate that microorganisms can reduce the unstable aliphatic hydrocarbon side-chain structure in coal through oxidation, decarboxylation, and enzyme catalysis and promote coal graphitization. (2) After microbial treatment, the fitting peak areas of hydroxyl groups, oxygen-containing functional groups, and aromatic hydrocarbons in the coal samples decreased substantially, with the fitting peak areas of hydroxyl groups and aliphatic hydrocarbons decreasing by 43.21% and 55.56%. This finding indicates that microorganisms tremendously affect the mechanism of oxidative spontaneous combustion of coal by reducing the number of functional groups and the generation of free radicals. (3) After microbial treatment, the characteristic temperature points of the coal samples shifted to the higher-temperature region in the TGA curve, and changes in the maximum thermogravimetric rate temperature and burnout temperature were the most significant, which were increased by 67.87℃ and 138.67℃, respectively. These results indicate that microorganisms greatly improve coal's thermal stability and resistance to oxidation and effectively inhibit its low-temperature oxidation process. Conclusions: Microbial treatment of coal samples changes their microcrystalline structures and promotes their orderliness and graphitization. The number of functional groups in coal and the coal's oxidation activity are considerably reduced. In addition, microorganisms improve the thermal stability and oxidation resistance of coal, slow its oxidation rate, and effectively inhibit its low-temperature oxidation process. These results provide a scientific basis for inhibiting spontaneous coal combustion through microbial action and provide a reference for the greening and diversification of the corresponding prevention strategies.