A series of cyclodextrin-based polypseudorotaxanes (PPRs) were constructed by threading native beta-cyclodextrin or l-tryptophan-modified beta-cyclodextrin onto the amino-terminated PPG chains of different lengths. Subsequently, these PPRs were further assembled to form netlike supramolecular aggregates through the linkage of gold nanoparticles, and the resulting water-soluble Au-PPR aggregates were comprehensively characterized by FT-IR, UV, NMR, fluorescence spectroscopy, powder X-ray diffraction patterning, TG-DTA, and transmission electron microscopy. The results showed that the size and sedimentation rate of the Au-PPR aggregates were mainly dependent on the lengths of the PPG chains. Significantly, the Au-PPR aggregate 8, involving many l-tryptophan residues, showed not only a satisfactory water solubility but also a good capturing ability for fullerenes in aqueous solution. The 8-fullerene conjugate thus formed exhibited a good DNA cleavage ability under light irradiation.