Effects of N and S functionalities on co-adsorption of CH4 + N-2 and CH4 + CO, on the coal vitrinite macromolecule model (CVMM) were explored using molecule simulation. Inclusion of the sulfoxide, amine, and sulfide functionalities can enhance S-CO2/CH4 (selectivity of CO2 over CH4), while the pyrrole and pyridine functionalities could not. The higher mole fraction of CO2 could reduce the pressure required to reach the stable equilibrium state as well as S-CO2/CH4. Microporous calculation results suggest that the microporous size distribution (MSD) of amine-CVMM (median pore size, D-M, 8.24 angstrom; free volume probed by He, V(F)d, 7105.55 angstrom(3)/cell) and sulfoxide CVMM (D-M, 7.92 angstrom; V-d(F), 7812.96 angstrom(3)/cell) are most suitable for CH4 adsorption, followed by pyrrole-CVMM (D-M, 7.18 angstrom; V-d(F), 6812.96 angstrom(3)/cell). The inclusion of N and S functionalities can distinctly increase the adsorption affinity of the linear molecular configurations of adsorbates by changing the adsorption orientations. The target N and S functionalities in functionalized CVMMs contribute primarily to the adsorption process of these three gaseous adsorbates. The adjacent functionalities have critical influences on adsorption affinity for these three adsorbate species depending upon the relative adsorption affinity strength of the adjacent functionalities and the target functionalities.