We report a computational study for cation characterization and CO2 capture in Li+-exchanged metal-organic frameworks (Li+-MOFs). Density functional theory is adopted to optimize cation locations and evaluate atomic charges, and molecular simulation is subsequently used to examine the separation of CO2/H-2 and CO2/N-2 mixtures for pre- and post-combustion CO2 capture. The cations are observed to locate near the carboxylic O-donors of metal clusters. Specifically, H+ ions in dehydrated Li+-MOF form covalent bonds with the O-donors, and H3O+ ions in hydrated Li+-MOF form hydrogen bonds with the O-donors. CO2 is overwhelmingly adsorbed over H-2 and N-2 in both dehydrated and hydrated Li+-MOFs. Adsorption occurs preferentially near the cations and metal clusters, which possess strong electrostatic potentials, and then in the square channels. At ambient condition, the selectivity is approximately 550 for CO2/H-2 mixture and 60 for CO2/N-2 mixture, higher than that in nonionic MOFs and other nanoporous adsorbents. The charges of framework and cations have a significant effect on the selectivity, which is found to decrease by 1 order of magnitude by switching off the charges. The hydration of cations in Li+-MOF leads to a reduced free volume and consequently a lower extent of adsorption.