Numerous experimental investigations indicated that expansive clays such as montmorillonite can intercalate CO2 preferentially into their interlayers and therefore potentially act as a material for CO2 separation, capture, and storage. However, an understanding of the energy-structure relationship during the intercalation of CO2 into clay interlayers remains elusive. Here, we use metadynamics molecular dynamics simulations to elucidate the energy landscape associated with CO2 intercalation. Our free energy calculations indicate that CO2 favorably partitions into nanoconfined water in clay interlayers from a gas phase, leading to an increase in the CO2/H2O ratio in clay interlayers as compared to that in bulk water. CO2 molecules prefer to be located at the centers of charge-neutral hydrophobic siloxane rings, whereas interlayer spaces close to structural charges tend to avoid CO2 intercalation. The structural charge distribution significantly affects the amount of CO2 intercalated in the interlayers. These results provide a mechanistic understanding of CO2 intercalation in clays for CO2 separation, capture, and storage.