Clathrate hydrates are a highly prospective material in energy and environmental fields, but the inherent nature of inclusion phenomena occurring in the stacked water cages has not been completely resolved yet. Investigating the magnetism of guest molecules is a new experimental approach in clathrate hydrate research to open the possibility of icy magnetic applications as a novel material as well as to understand the unrevealed host guest interactions in icy inclusion compounds. In this study, we observed an indirect spin coupling between encaged dioxygen molecules via a nonmagnetic water framework through the measurement of guest magnetization. This spin coupling is reminiscent of superexchange coupling between magnetic ions through intervening oxygens in antiferromagnetic oxides, such as MnO and CoO. Theoretical calculations revealed that OH(-) incorporated in the framework induced the mixing of perpendicular pi* orbitals of two distant dioxygens and that ammonia doping into the hydrate cage leads to a longer lifetime of that orientation.