Given that SOF materials have both inorganic and organic properties and are easy to prepare and structurally designable, this paper carries out the microbehavioral analysis and membrane design of SOF-8, SOF-9, and SOF-10 membranes for the hydrogen purification process of RMFCs. Since three materials have complementary performance characteristics for hydrogen purification, this paper focuses on the gas separation behavior of these three composite membranes using molecular dynamics simulations. Results showed that the SOF-9a+10a composite membranes could 100% block CO2 and CO, and displayed an excellent H2 permeability of 6.118 × 105 GPU during H2/CO2 separation, which exceeded the industry standard by nearly 105 times. Additionally, the SOF-9a+8 and SOF-10a+8 composite membranes improved gas selectivity and maintained high H2 permeability. Moreover, microdiffusion analyses revealed that the small pore sizes and irregular-shaped pore channels effectively hindered CO2 and CO transport. Microscopic analysis shows the potential of SOF composite membranes for gas separation.