Clathrate hydrates are crystalline compounds consisting of hydrogen-bonded host water frameworks that eventually structure polyhedral cages. We suggest for the first time their potential as nano-reactors in which target reactions can occur. The energetics of one-dimensional CO radical cation (CO·+) transfers through the hexagonal faces of sI large cages are closely examined to verify the reaction concept in an icy confined space. The barrier energies for migrating a CO radical cation from the cage center to the edge of the hexagonal face are estimated to be 87 and 311 kJ/mol according to calculations with the B3LYP 6-311+G (d, p) basis set, significantly depending on the orientation of the radical. These results indicate that the barrier energy increases sharply when the CO radical cations are oriented parallel to the cage’s hexagonal face. In the parallel migration mode, the hydrogen-bonded water networks are repulsed by electron clouds of CO·+ located on the same plane; thus, the repulsion forces induce a significant increase in the barrier energies. Further, we used separate basis sets of high and low levels processed by the ONIOM scheme for the effective calculation of the entire cage structure of the clathrate hydrates with guest molecules. The calculation run time was significantly shortened when the ONIOM scheme was adopted, while a difference in the barrier energy of approximately 5% was observed compared to the full-scale calculation with a high-level basis set.