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Herein, we report the facile conjugation between proteins and water-soluble [60]fullerene derivatives (DC60) under native conditions using SpyTag as a reactive handle. Water-soluble [60]fullerene derivatives were first prepared via sequential Bingel-Hirsch reaction and “clicked” with SpyTag to give DC60-SpyTag for native conjugation with proteins by the highly efficient SpyTag-SpyCatcher chemistry. The bioconjugation was confirmed by MALDI-TOF MS spectra and SDS-PAGE analysis. The TEM and UV-vis spectroscopic study further revealed that the DC60 could alter the optical performance and induce aggregation of the target proteins. It thus provides a general and robust method for modifying proteins with C60 derivatives and could potentially be adapted for native conjugation between proteins and other nonbiological motifs as well.