The discovery of buckminsterfullerene (C60) marked a significant milestone in exploring three-dimensional carbon materials. However, exponentially increasing isomerism on higher fullerenes pose a considerable challenge in their recognition and separation. Herein, we designed two pseudo-cubic metal-organic cages (MOCs, T and S4) with distinct cavity microenvironments, which showcase remarkable recognition specificity toward higher fullerene isomers. Compared to cage T, a symmetry shift from S4 to C2 emerges upon encapsulating an ellipsoidal D2-C76 guest, due to the precise shape matching curtails guest rotation. Furthermore, cage S4 demonstrates heightened sensitivity toward distinguishing a pair of highly similar constitutional isomers of C2v-C78. The approach of reducing symmetry positions MOCs as promising candidates for encapsulating and identifying a broader spectrum of fullerene isomers, paralleling the selectivity observed in biological systems.