Biodegradable polyrotaxanes (PRXs) were synthesized from bis-amino-terminated poly(L-lactide) (PLLA) and alpha-cyclodextrin (alpha-CD), combined with capping by bulky end groups at the amino-termini of PLLA through enzymatically cleavable peptide linkages. The crystalline structure of the PRXs in the solid state was investigated by wide-angle X-ray diffraction (WAXRD), and the results suggested that PRX forms a column-type crystalline structure. Hydrolysis of ester bonds of the PLLA in PRX was prevented due to the supramolecular structure. However, in the presence of a protease (papain), the hydrolysis of PLLA in PRX was induced. The removal of the bulky end groups by the protease acted as a trigger for the release of alpha-CD and allowed hydrolysis of the PLLA ester bonds. Such unique hydrolysis behavior, that is, proteinase-triggered degradation of a polyester, was achieved by the combination of the supramolecular architecture, biodegradable PLLA, and enzymatically cleavable end groups.