Adsorption of methane and nitrogen, in pure and mixture states, on faujasite (FAU) zeolite was investigated by molecular dynamics (MD) simulation. FAU zeolite with Si/Al ratios of 1, 2, and 3 was tested to evaluate the effect of changes in the zeolite structure. Adsorption isotherms of methane and nitrogen were derived using MD simulation with COMPASS force field at various temperatures and pressures and the results were compared with experimental data. Methane/nitrogen selectivity was calculated to analyze the separation performance of FAU zeolite. Under all tested conditions, the calculated selectivities were higher than 2, which was in the acceptable range for separation. Diffusivity of the gases in the zeolite structure was assessed using mean square displacement analysis. The results demonstrated that a lower Si/Al ratio in the FAU structure yield higher methane adsorption.