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The isolation of multiple-isomers of Sc2@C80 (Ⅰ, Ⅱ, Ⅲ) endohedral metallofullerenes is reported for the first time. The new C80-based Sc-metallofullerenes are characterized by UV-Vis-NIR absorption spectroscopy and detailed chromatographic retention time data. A close relationship between the isomer structure and the corresponding HPLC retention time of the metallofullerenes is presented.