Abstract: As a core setting for carbon reduction and emission control in the energy sector, achieving efficient carbon sequestration after coal mining has become a primary challenge in the development of green mining practices. Meanwhile, as an available underground space resource, the substantial carbon storage potential of goaf provides broad application space for carbon reduction in coal mines. Coal mine environments naturally harbor enriched microbial communities. Applying microbial technology for carbon sequestration in goaf represents a new technological pathway for promoting green and low-carbon development of mines. Therefore, a strategy utilizing indigenous microorganisms in goaf for synergistic carbon fixation with residual coal was proposed. Two carbon-fixing bacterial strains, Pseudomonas aeruginosa and Pseudomonas phenolnatrix, were isolated and screened from underground soil in the goaf. Single-factor experiments were conducted to optimize the growth conditions of the strains and to investigate the effects of cultivation time and initial CO₂ volume fraction on their carbon fixation capacity. Furthermore, the evolution of pore structure and changes in the composition of chemical functional groups in coal samples before and after microbial treatment were systematically analyzed to elucidate the synergistic carbon fixation mechanism between indigenous microorganisms and residual coal in the goaf. The results showed that after 48 h of cultivation under an initial CO₂ volume fraction of 15%, the carbon fixation rates of the two strains reached 98.13% and 98.67%, respectively, demonstrating that the microorganisms exhibited high carbon fixation efficiency. It also indicated that in a closed space, the carbon fixation rate cannot be improved solely by extending the microbial metabolic time. After the changes in pore structure of the coal samples, the total intrusion volume increased to 0.732 2 mL/g and 0.746 9 mL/g, respectively, and the total pore volume growth rates reached 22.33% and 24.79%, respectively. Fractal characteristics indicated that after microbial treatment, the porosity of the coal samples increased markedly, the pore structure became more complex, and the coal surface became rougher, providing more adsorption sites and channels for CO₂ adsorption. Changes in functional groups showed that the proportion of self-associated hydroxyl groups in the coal samples increased to 24.06%, the proportion of trisubstituted benzene rings increased to 32.51%, while the proportion of aliphatic hydrocarbon functional groups decreased markedly, indicating that different carbon-fixing microorganisms exerted distinct effects on coal functional groups through their metabolic activities, resulting in varying trends of increase or decrease in their abundances. The optimal growth conditions and carbon fixation performance of indigenous carbon-fixing microorganisms in goaf were determined, the mechanism by which microorganisms modify coal pore structure and regulate functional group composition through metabolic activities was elucidated, and the synergistic effect between microbial carbon fixation and enhanced CO₂ adsorption by coal was achieved, providing a new approach for CO₂ sequestration in coal mine goaf.