Using MD simulation, a series of porous graphene and zinc oxide membranes were designed to separate the H2/H2S mixture gas. Then, the effect of pore size and temperature increase on the rate of gas separation was investigated. The diffusion process, which is one of the most important parameters for measuring the separation of H2 and H2S gas molecules in the porous adsorbents of graphene and zinc oxide, was evaluated at different temperatures. The calculations showed that the penetration of H2 gas molecules due to the uniform distribution on the surface of the adsorbents, by spreading on the membrane, can find the pores more effectively. The simulation results showed that the penetrability and selectivity of the gas molecules are directly related to the pore size, due to the size limitation, only a small amount of hydrogen molecules can pass the minimum pore size (4.929 Å). In this study, the highest penetrability for graphene and zinc oxide nanoparticles was 22% and 46%, respectively. At pores smaller than 13.432 Å, a high degree of selectivity was reported. Also, with increasing pore size on graphene and zinc oxide sheets, a decrease in selectivity was observed. Temperature is another parameter that has been tested in the simulation and shows that its increase has a significant effect on the adsorption of gas molecules so that with increasing temperature, the amount of adsorption on the adsorbent surface decreases. This is because the adsorption process is exothermic. The highest adsorption energy was related to H2S gas with −892.81 kcal/mol in graphene and the lowest was −268.31 kcal/mol for H2 gas in ZnO adsorbent. The results of this study can be used to design industrial applications and reduce environmental impact.