The characteristic behavior of alcohol guest inclusions and interactions occurring within binary cyclobutanemethanol (CBM)+methanol (MeOH) and cyclopentanemethanol (CPeM)+MeOH hydrates with hydrate lattices consisting of NH4F and H2O was investigated using crystal structure analysis with Rietveld refinement. The crystal structure of our hydrate systems was in the cubic Fd-3m space group. CBM or CPeM was captured within the large 51264 cages of structure II (sII) hydrates, but the effective molecular size of CBM and CPeM was larger than the large cavity size of common sII hydrates. Therefore, the hydroxyl moiety of the CBM and CPeM could interact with the host framework of clathrate hydrates via hydrogen bonding. Similarly, MeOH was encapsulated within the small 512 cages of the sII hydrates, but the Rietveld analysis results indicated that the thermal displacement parameters of the encapsulated MeOH were abnormally high, suggesting off-centered positioning of MeOH and potential host-guest interaction within the small 512 cages of the sII hydrates. These results provide useful insight into the complex nature of host-guest inclusion chemistry.