The adsorption of hydrogen sulfide (H2S), carbondioxide (CO2) and methane (CH4) on H-FER zeolite was investigated under computational chemistry using ONIOM (HF/6-31G (d,p):UFF) and ONIOM (B3LYP/6-31G (d,p):UFF) method. Compared to the H-FER zeolite induces much stronger binding of H2S, CO2 and CH4 suggesting great enhancements in the adsorption selectivity. The order of binding energies of adsorbed molecules is H2S > CO2 > CH4. It was found that the extended zeolitic framework covering the nanocavity was essential for describing the confinement effect of the zeolite. The results of these calculations show that the zeolite can be used to adsorb H2S bester then CO2 and CH4. Carbondioxide and hydrogen sulfide are pollutant in biogas product from anaerobic digestion of biodegradable materials. There for, zeolite can be use to purified gas before using as fuel.