To explore the effect of different functional group fractures in coal on the adsorption characteristics of CH4, molecular models of bituminous coal (Wiser) with fractured oxygen-containing functional groups (W–O5), sulfur-containing functional groups (W–S5), and nitrogen-containing functional groups (W–N5) were constructed. The microscopic mechanism by which the fracture of different functional groups in bituminous coal molecules affects CH4 adsorption was analyzed using Density Functional Theory (DFT), Molecular Dynamics (MD), and Grand Canonical Monte Carlo (GCMC) methods. The results show that functional groups facilitated the polarization of CH4 during the adsorption process, with the following influence relationship: oxygen-containing functional groups > sulfur-containing functional groups > nitrogen-containing functional groups; Fracturing functional groups in bituminous coal molecules weakened the adsorption capacity and reduced adsorption sites of CH4, the sequence of CH4 adsorption was Wiser > W–N5 > W–S5 > W–O5. High temperature reduced the effect of nitrogen-containing functional group fractures on CH4 adsorption, but had no obvious effect on sulfur-containing and oxygen-containing functional groups. The interaction between CH4 and the coal molecule decreased after functional group fractures, causing the enhanced diffusion of CH4 on bituminous coal molecules, and the order was W–O5 > W–S5 > W–N5 > Wiser. Additionally, the fracture of functional groups decreased the pore size of the bituminous coal molecules, which inhibited CH4 adsorption but facilitated its diffusion. The research provides theoretical support for enhancing CH4 desorption and improving the recovery rate of coalbed CH4.