Separation and capture technology for small molecules is of great significance, including for the goal of adsorbing and separating CO2. Accurately controlling the pore size to achieve separation of molecules with similar sizes remains a challenging task in rigid porous materials, such as inorganic zeolites. We propose precise pore size engineering of "larger pore" faujasite (FAU) zeolite by depositing carbon atoms inside its framework. Low-dose electron microscopy with high spatial resolution is used to visualize the carbon deposition process and the corresponding evolution of pore size. Pore size changes as a function of carbon deposition time are also studied by gas adsorption using N2. The carbon-modulated FAU samples with optimized pore sizes exhibit excellent gas separation of CO2 relative to other small molecules. For a 50/50 H2/CO2 mixture, the separation factor was increased by 31% with a breakthrough time difference over 1200 s/g as compared to the neat FAU. We thus tailor the gas adsorption of FAU through partial filling of pores with deposited carbon and note that this can be generalized for the pore size engineering of many porous materials for use in industrial gas separation applications.