Endohedral metallofullerenes (EMFs) containing actinides are rather intriguing due to potential Sf-orbital participation in the metal-metal or metal-cage bonding. In this work, density functional theory calculations first characterized the structure of recently synthesized ThC74 as Th@D-3h (14246)-C-74. We found that the thorium atom adopts an unusual off-axis position inside cage due to small metal ion size and the requirement of large coordination number, which phenomenon was further extended to other Th-based EMFs. Significantly, besides the strong metal-cage electrostatic attractions, topological and orbital analysis revealed that all the investigated Th-based EMFs exhibit obvious covalent interactions between metal and cage with substantial contribution from the Th 5f orbitals. The encapsulation by fullerenes is thus proposed as a practical pathway toward the f-orbital covalency for thorium. Interestingly, the anomalous internal position of Th led to a novel three-dimensional metal trajectory at elevated temperatures in the D-3h-C-74 cavity, as elucidated by the static computations and molecular dynamic simulations.