Gas sorption and molecular (ionic) storages are important functionalities in porous materials. In molecular porous crystal {{RuIII(H2bim)3­(TMA)}2·mH2O} n , the hydrophilic nanochannel accommodates the water nanotube (WNT) composed of a 4461074-polyhedral cage. The experiment on weight change reveals that the cage structure is maintained above 50% RH (relative humidity) at 294 K. As the relative humidity is reduced from 80 to 50% RH, the proton conductivity exponentially decreases from 0.02 to 0.01 (Ω cm)−1 owing to the dehydration of inner H2O molecules through WNT, which acts as a nanofluidic channel. Upon pressurizing Xe at 0.4 MPa for 50% RH, the proton conductivity exponentially decreases and approaches 0 (Ω cm)−1. The infrared and 129Xe-NMR experiments make clear that Xe together with about 25H2O molecules per cage are stabilized in WNT at low pressures compared to Xe-clathrate hydrate. Those results experimentally demonstrate that the Xe hydrate inhibits the proton conduction. The formation of Xe hydrate is characterized by fast and slow processes with a translational diffusion constant of 1 × 10–10 and 6 × 10–12 m2/s, respectively. The reorganization and hardening of the hydrogen-bonding water network are considered to diminish the conducting pass of proton, and to reduce the protonic transfer from H3O+ to adjacent H2O.