CH4 adsorption can deform coal microporous structures, subsequently altering adsorption isotherms. To unravel this intricate interplay at a microscopic level, we use a hybrid Grand Canonical Monte Carlo/Molecular Dynamics (GCMC/MD) simulation at 313.15 K and pressures up to 500 bar on five independent amorphous coal matrix models. Our results reveal that CH4 adsorption increases pore volume and porosity primarily by generating additional pores of similar sizes to those present in coal matrices, thereby maintaining a consistent average pore size across different pressures. The volumetric strain has a linear correlation with CH4 loading, with volumetric swelling amount approximating the expansion of CH4-occupiable pore volume, but less than He-occupiable pore volume which results in increased matrix skeletal density. Local radial density distribution of carbon atoms indicates that the immediate environment around carbon atoms remains unchanged. In a flexible matrix, the energy released during CH4 adsorption is partially absorbed by matrix deformation, resulting in a lower isosteric heat of adsorption compared to a rigid matrix, which suggests easier desorption. This study provides new insights into the mutual relationship between CH4 adsorption and coal matrix deformation, shedding lights on the complex interactions of various hydrocarbons with geomaterials.