To guarantee the safety and sustainability of coal mining by effectively mitigating the substantial risk associated with coal spontaneous combustion, this study proposes a multifaceted prevention strategy aligned with green environmental principles. A compound flame retardant with a physicochemical control mechanism was prepared using indigenous microorganisms to mineralize residual coal after mining, utilizing Bacillus pasteurelli as a substitute material for inorganic salts. Under laboratory conditions simulating coal self-combustion, biobased flame retardants were employed to investigate the physical and chemical transformations of heat and mass evolution from ambient temperature to combustion in two representative low-rank coals. By quantitatively comparing alterations in microbiome-based groups among raw lignite, bioretarded lignite, and two control samples, the inhibitory mechanism of biobased materials on the oxygen reaction pathway was elucidated. The findings substantiated that biobased modification can consolidate the methyl and methylene groups present in aliphatic hydrocarbon side chains, which are prone to instigating low-temperature oxidation reactions. Additionally, the preventive performance of biobased flame retardants was assessed through temperature-programmed experiments, which involved estimating the critical self-heating temperature, oxygen consumption, and gas production rates of compared coal samples. The results demonstrated significant enhancements in the resistance to spontaneous combustion following bioretarded modification. Notably, the identification grade of long flame coal shifted from easy to moderate susceptibility to spontaneous combustion. Furthermore, biobased flame retardants exhibited remarkable flame retardancy rates of approximately 80% for lignite, thereby validating their efficacy as more environmentally friendly and technologically advanced substitute materials for inhibiting spontaneous combustion in low-rank coals.