The reaction mechanism and origin of regioselectivity of (2 + 2) cycloadditions of benzyne to endohedral metallofullerenes M3N@C80 (M = Sc, Y) were investigated with density functional calculations. The reaction was demonstrated to follow a diradical mechanism rather than a carbene mechanism, in which the formation of the diradical intermediate is the rate-determining step. Through rotation of benzyne moiety on the fullerene surface, the diradical intermediate on 566 site could isomerize to two new diradical intermediates which give rise to two distinct [5,6] and [6,6] benzoadducts, respectively. However, the diradical intermediate on 666 site only produces the [6,6] benzoadduct. The nature of the endohedral cluster not only influences the regioselectivity, but also determines the cycloadduct geometry. For Sc3N@C80, the [5,6] benzoadduct is preferred kinetically and thermodynamically, whereas in the case of Y3N@C80, both [5,6] and [6,6] benzoadducts are favorable. In contrast to closed-cage benzoadducts of Sc3N@C80, Y3N@C80 affords open-cage benzoadducts, making it the first example that the endohedral cluster could alter cycloadducts from the closed cage to open cage. With further analysis, it is revealed that the origin of regioselectivity results from the local strain energy of the fullerene cage.