Neutron powder diffraction data of deuterated clathrate hydrates of carbon dioxide and xenon were measured in order to investigate the effects of the motion of guest molecules on the structure of the surrounding hydrogen-bonded network. Rietveld analysis revealed that the magnitude of the thermal parameters of the host atoms of the CO₂ clathrate hydrate depends strongly on the crystallographic site, while those of the Xe clathrate hydrate do not depend on the site. The host lattice structure of the Xe clathrate hydrate may be a close representation of the hypothetical empty clathrate hydrate, because of the simple spherical shape of the Xe molecule. The site dependence of the thermal parameters of the host atoms in the CO₂ clathrate hydrate are attributed to the motion of the CO₂ molecules in the cages. The CO₂ molecule rotates anisotropically about the symmetry axis inside the tetrakaidecahedral cage. We suppose that the surrounding deuterium atoms are temporarily attracted and released by the oxygen atoms of the rotating CO₂ molecule and so their thermal parameters are large. It is concluded that the interaction between the guest molecule and the surrounding host atoms is so strong that the thermal vibrations of the host atoms are affected by the motion of the guest molecules inside the cages.