Acid clathrate hydrates which do not contain hydrogen fluoride impurities are believed to include several vacancy sites in the host lattice for protonation of the framework. In this work, the crystal structures of a DClO4·5.5D2O solid at various temperatures were identified by the direct space method and Rietveld refinement of the neutron powder diffraction patterns. A position change of vacancy sites accompanying the shift of ClO4- guest ions in the 51262 cavity toward the center of the cavity from the edge of the hexagonal face was observed at about 180 K, and this phenomenon is expected to result in weakened host proton-guest anion interactions and to induce a phase transition related to the proton conduction behavior of the DClO4 clathrate. The present findings explain the proton dynamics of the hydrogen fluoride-free acid clathrate hydrates and provide a better understanding of the nature of guest-host interactions occurring on ion-doped hydrate materials.