Under photoirradiation, Sc3N@Ih-C80 reacted readily with disilirane 1, silirane 4, and digermirane 7 to afford the corresponding 1:1 adducts, whereas Sc3N@D5h-C80 was recovered without producing those adducts. Based on these results, we described a novel method for the exclusive separation of Ih and D5h isomers of Sc3N@C80. The method includes three procedures: selective derivatization of Sc3N@Ih-C80 using 1, 4, and 7, facile HPLC separation of pristine Sc3N@D5h-C80 and Sc3N@Ih-C80 derivatives, and thermolysis of Sc3N@Ih-C80 derivatives to collect pristine Sc3N@Ih-C80. In addition, laser flash photolysis experiments were conducted to elucidate the reaction mechanism. Decay of the transient absorption of 3Sc3N@Ih-C80* was observed to be enhanced in the presence of 1, indicating the quenching process. When Sc3N@D5h-C80 was used, the transient absorption was much less intensive. Therefore, the quenching of 3Sc3N@D5h-C80* by 1 could not be confirmed. Furthermore, we applied time-dependent density functional theory (TD-DFT) calculations of the photoexcited states of Sc3N@C80 to obtain insights into the reaction mechanism.