The spontaneous combustion of coal in goaf is the main cause of mine fire at present. Lignite has become a major hidden danger in mine production safety because of its easy oxidation. In this paper, an innovative strategy was proposed to inhibit the spontaneous combustion of lignite by using the principle of microbial-induced calcium deposition. Based on the optimized culture method, a novel composite inhibitor of Bacillus pasteurelli was prepared. SEM, pore size analysis and FT-IR experiments were carried out simultaneously, and the oxidation properties of lignite before and after inhibition were quantitatively characterized from the perspective of microstructure, and the flame retardant properties of microbial and chemical retardants on coal samples were compared. The results show that a large number of deposited calcium carbonate particles are obviously attached to the surface of lignite after microbial inhibition treatment, which plays a physical oxygen insulation role. At the same time, the total pore volume and specific surface area of the coal sample decreased by 68.49% and 74.01%, respectively, indicating that microbial inhibitors can effectively plug the primary pores of lignite. Based on the peak measurement of 400-4000cm-1 infrared spectrum of coal samples, it is found that the contents of active groups including hydroxyl, carboxyl and methyl/methylene in lignite molecules after microbial inhibition are lower than those in raw coal, especially the methyl/methylene content involved in the initial oxidation reaction decreased by 96.5% compared with the baseline content in raw coal. The results show that the oxidation and self-heating capacity of lignite after microbial inhibition is effectively restrained in the initial spontaneous combustion. The research results of this paper can provide effective solutions for the prevention and control of coal spontaneous combustion risk in mined-out area.