The effects of chemical and structural surface heterogeneity on the CH4 adsorption behaviour on microporous carbons have been investigated using a hybrid theoretical approach, including the use of density functional theory (DFT), molecular dynamics (MD), and grand canonical Monte Carlo (GCMC) simulations. Bader charge analysis is first performed to analyze the surface atomic partial charges. The CH4 adsorption densities in defective and functionalized graphite slit pores are lower than that in the perfect pore according to the MD simulations. Finally, the CH4 adsorption isotherms for the perfect, defective and functionalized slit pores are analyzed using the GCMC simulations in combination with the DFT and MD results. For pores with a defective surface, the adsorption capacities decrease; the embedded functional groups decrease the adsorption capacity at low pressure and enhance it at high pressure. Our results demonstrate the significant effects of chemical and structural surface heterogeneity on the CH4adsorption and provide a systematic approach to understand the gas adsorption behaviour.