Endohedral metallofullerenes (EMFs), namely fullerenes with metallic species encapsulated inside, represent an ideal platform to investigate metal–metal or metal–carbon interactions at the sub‐nanometer scale by means of single‐crystal X‐ray diffraction (XRD) crystallography. Herein, recent progress in the identification of new structures and unprecedented properties are discussed according to the categories of monometallofullerenes, dimetallofullerenes, carbide clusterfullerenes, and nitride clusterfullerenes. In particular, the dimerization and the cage‐isomer dependent oxidation state of the inner metal atom are summarized in terms of pristine monometallofullerenes. Metal–metal bonds involving lanthanide–lanthanides or actinide–actinides are discussed based on both experimental and theoretical studies. The cluster–cage matching and/or mutual selections, as well as the rarely seen M=C double bonds, are discovered in M2C2@C2n, U2C@C80, M2TiC@C80, and Ti3C3@C80. Subsequently, the geometries of different M3N clusters in various cages are discussed, revealing size‐matching between the internal M3N cluster and the outer cage induced by the planarity of the cluster. Finally, an outlook regarding the future developments of the molecular structures and applications of EMFs is presented.