To verify the accuracy and rationality of the molecular simulation model, the microscopic mechanism of gas adsorption was analyzed and clarified from a microscopic perspective. The effect of molecular models created by direct construction and supercell expansion on the adsorption capacities of CH4 and CO2 has been analyzed. Eight coal-based molecular configurations were created to simulate the isothermal adsorption process of CH4 and CO2 using various coal-based molecular configurations. Using physical experiments, the validity of different construction methods for coal-based molecular structures was verified. The direct construction method was chosen to simulate the effect of various coal-based molecular numbers on the adsorption capacity of CH4 and CO2. The results show that the adsorption capacity of CO2 on coal is greater than that of CH4. The isothermal adsorption curves of CH4 and CO2 in coal-based molecular systems constructed using different methods reveal that the adsorption of methane on coal molecules adheres to the Langmuir monolayer adsorption theory. The adsorption sites for methane increase with the rise in free volume. The structure directly constructed and the supercell expansion directly determines the amount of methane adsorbed by each coal based molecule. The adsorption constants of CH4 and CO2 on the supercell extended structure are more volatile than those on the directly constructed structure, and the structure constructed directly for different coal based molecules is better than the supercell extended structure. The simulation using the direct construction method shows that as the number of coal-based molecules in the molecular configuration increases, The isothermal adsorption quantities of CH4 and CO2 increase linearly. The molecular configuration is not affected by the number of anthracite molecules. Molecular configuration is not affected by the number of anthracite molecules. The rationality of model construction has no obvious relationship with the number of coal based molecules.