Carbon dioxide (CO) and hydrogen sulfide (HS) as harmful gases are always associated with methane (CH) in natural gas, biogas, and landfill gas. Given that chemisorption and physisorption are the key gas separation technologies in industry, selecting appropriate adsorbents is crucial to eliminate these harmful gases. The adsorption of CH, CO, and HS has been studied based on the density functional theory (DFT) in this work to evaluate the feasibility of transition metal (M = Mn, Fe, Co, Ni, Cu, Mo) porphyrin-like moieties embedded in graphene sheets (MN-GPs) as adsorbents. It was found that the interactions between gas molecules and MN-GPs (M = Mn, Fe, Co, Ni, Cu, Mo) are different. The weaker interactions between CH and MN-GPs (M = Co, Ni, Cu, Mo) than those between CO and MN-GPs or between HS and MN-GPs are beneficial to the separation of CH from CO and HS. The maximum difference in the interactions between gas molecules and MoN-GPs means that MoN-GPs have the greatest potential to become adsorbents. The different interfacial interactions are related to the amount of charge transfer, which could promote the formation of bonds between gas molecules and MN-GPs to effectively enhance the interfacial interactions.