Abstract Herein we report the spectroscopic, electrochemical, TEM and DLS characterizations of C60 supramolecular inclusion complexes with α‐, β‐and γ‐cyclodextrins prepared using anionic C60. The results indicate that the cyclodextrin itself has little effect on the encapsulated C60 or on the properties of the inclusion complex. Instead, the cyclodextrin has a significant influence on the aggregation behavior of individual complex in aqueous solution, which in turn affects the property of the supramolecular complex of cyclodextrin and C60 greatly. As the cavity dimension of cyclodextrin becomes smaller as it changes from γ‐CD to β‐CD, and finally to α‐CD, it is observed that more aggregation occurs for the corresponding inclusion complex in aqueous solution.