The crystal structure of deuterated methane hydrate (structure I, space group: Pm(-)3n) was investigated by neutron powder diffraction at temperatures of 7.7-185 K. The scattering amplitude density distribution was examined by a combination of Rietveld method and maximum entropy method (MEM). The distribution of the D atoms in both D(2)O and CD(4) molecules was clarified from three-dimensional graphic images of the scattering amplitude density. The MEM results showed that there were low-density sites for the D atom of D(2)O in a particular location within the D(2)O cage at low temperatures. The MEM provided more reasonable results because of the decrease in the R factor that is attainable by this method. Accordingly, the low-density sites for the D atom of D(2)O probably exist within the D(2)O cage. This suggests that a spatial disorder of the D atom of D(2)O occurs at these sites and that hydrogen bonds between D(2)O molecules become partially weakened. With regard to the CD(4) molecules, there were high-density sites for the D atom of CD(4), and the density distribution of the C and D atoms was observed separately in the scattering amplitude density image. Consequently, the C-D bonds of CD(4) were not observed clearly because the CD(4) molecules had an orientational disorder. The D atoms of CD(4) were displaced from the line between the C and O atoms, and were located near the face center of the polygon in the cage. Accordingly, the D atoms of CD(4) were not bonded to specific O atoms. This result is consistent with the hydrophobicity of the CD(4) molecule. We also report the difference between the small and the large cages in the density distribution map and the temperature dependence of the scattering amplitude density.