The most common fullerene member C60 displays many biological applications, such as, anticancer, human immunodeficiency virus and hepatitis C virus inhibitors, O2 uptake inhibitor and vectors for drug and DNA. Nevertheless, the innate hydrophobicity of C60 constrains its further development. We introduced cyclodextrins to enhance the water-solubility of C60. Nine cyclodextrin-C60 conjugates, including seven α-cyclodextrin-C60 conjugates and two γ-cyclodextrin-C60 conjugates, were designed and synthesized. All of these conjugates did not show obvious cytotoxicity. The anti-influenza virus activity of nine conjugates was assessed. Two γ-cyclodextrin-C60 conjugates, which were relatively more water-soluble, exerted higher inhibition with IC50 values of 87.73 µM and 75.06 µM, respectively, than seven α-cyclodextrin-C60 conjugates.