Acetylation of biodegradable polyrotaxanes was examined to estimate the effect on its supramolecular dissociation via terminal ester hydrolysis. The biodegradable polyrotaxanes, in which many alpha-cyclodextrins (alpha-CD) are threaded onto a poly(ethylene glycol) chain capped with L-phenylalanine via ester linkages, were acetylated using acetic anhydride; alpha-CD release behavior was then characterized by in vitro hydrolysis. The degree of acetylation was changed by the concentration of acetic anhydride and the reaction time. The results of the in vitro hydrolysis indicate that the critical degree of acetylation to prolong supramolecular dissociation lies at around 30%. The terminal hydrolysis proceeded completely even with 100% of acetylation. These findings suggest that the hydrophobization of alpha-CDs in the polyrotaxane makes it possible to delay the time to complete the supramolecular dissociation. The hydrophobization of the polyrotaxane is of great importance for designing implantable materials that maintain their supramolecular structure until tissue regeneration with complete terminal hydrolysis.