Based on the experimentally determined framework structure of porous MnO2 octahedral molecular sieve (OMS)-5, we used density functional theory-based calculations to evaluate the effect of Na+ cation on pore dimensionality and structural stability, and the interaction between CO2 and OMS-5. We quantified the formation energy of one CO2/unit tunnel and two CO2/unit tunnel, and projected the electronic density of states on the OMS-5 framework, CO2 molecules, and Na+ cations to reveal their individual contributions and bonding nature. Partial charge densities were also calculated to investigate CO2 adsorption behavior in the OMS-5. Our studies predict the initial stage and driving force for the adsorption of CO2 in the OMS-5, guiding the OMS material design for carbon capture and storage applications.