Abstract: Determining favorable factors in methane production from residual coal post-biohydrogen production holds great theoretical and practical significance for improving the efficiency of methane production in the second stage of coal-based poly-generation. This study focuses on residual coal after hydrogen generation through anaerobic fermentation. Using coal samples from the Baiyinhua open-pit mine in Inner Mongolia as fermentation substrates, this study explored the dynamic trends of both the methane production and structure of the residual coal under different conditions by altering the aeration conditions and hydraulic retention time (HRT). Key findings are as follows: (1) Among the experiment groups with different atmosphere conditions, the CO₂ group exhibited the highest methane production performance, with a unit gas production of 4.72 mL/g. In contrast, the gas production performance gradually decreased with an increase in the HRT. (2) The hydrogenase activity and gas production demonstrated similar laws of change. After reactions, all groups showed low chemical oxygen demand (COD) of the bacterial liquid. It is considered that CO₂ can enhance bacterial enzyme activity, leading to a more pronounced CO₂ methanation process. Besides, it can be inferred that a long HRT is not conducive to the survival of the microflora. Therefore, a short HRT is recommended the late engineering practices. (3) As discovered by the monitoring of the residual coal after anaerobic fermentation using X-ray powder diffraction (XRD) and Fourier transform infrared spectroscopy (FTIR), the coal samples exhibited the largest aromatic carbon layer spacing when CO₂ was introduced, with the numbers of some reactive functional groups, such as carboxyl and hydroxyl, in the coal decreasing. Under a HRT of 3 d, the microcrystalline structure and functional groups changed significantly. In contrast, a prolonged HRT corresponded to less pronounced changes in the coal structure. Therefore, injecting CO₂ can not only improve the gas production rate but also change the macromolecular structure and pore structure of coal, thus enhancing the permeability, expansion, infiltration, and degradation of the coal seams themselves. Furthermore, the integration of geologic CO₂ sequestration and coalbed methane bioengineering can be achieved.