Porous interpenetrated zirconium-organic frameworks (PIZOFs) with various functional groups are explored for CO2 capture using molecular simulation and experiment. Functionalization enhances the CO2 uptake and selectivity over other gases, but small cavities play an even more important role. Particularly at low pressures, small cavities enhance the CO2 adsorption density nearly 5 times greater than the functionalization. PIZOF-2 outperforms the other PIZOF structures for CO2 separation from methane and nitrogen (related to raw natural gas and postcombustion of coal mixtures) due to the combination of small cavities around 5 A in diameter and functionalized linkers with methoxy groups attached to the central ligand. The small cavities within the interpenetrated structures are crucial for achieving high selectivities, especially for cavities surrounded by a combination of 6 benzene rings, 2 metal clusters, and 4 methoxy groups that offer a tight overlapping potential energy field, ideal for catching CO2.