Concrete crystallographic results of endohedral metallofullerenes (EMFs) disclose that the bonding within the metallic clusters and the interactions between the metal ions and the cage carbon atoms, which are closely associated with the coordination ability of the metal ions, play essential roles in determining the stability, the molecular structure, and the chemical behavior of the hybrid EMF molecules, in addition to the previously recognized charge transfer from metal to cage. For the carbide cluster metallofullerenes, a "size effect" between the encapsulated metallic cluster and the fullerene cage has been suggested. Thus, through the geometric effect, a series of giant fullerenes (C90-C104) have been stabilized by encapsulating a large La2C2 cluster, which adopts different configurations in accordance with cage size and shape. Interestingly, the crystallographic analysis of La2C2@ D5(450)-C100 has led to the direct observation of the axial compression of short carbon nanotubes caused by the internal stress. Additionally, the defective C2(816)-C104 cage is viewed to be a precursor that can transform into the other three ideal tubular fullerene cages, presenting crystallographic evidence for the top-down formation mechanism of fullerenes. Structural characterization of Y2C2@C108 confirms a linear carbide cluster inside the large cage, indicative of a geometric effect of cage size on the bonding behavior of the internal cluster. Apart from the carbide realm, direct metal-metal bonding is observed between the two seemingly repulsive Lu2+ ions in Lu2@C82-86, adding new insights into current coordination chemistry. Meanwhile, the bonding state between the metal ions inside the cage (e.g., in La2@ I h(7)-C80) and even the configuration of the internal metallic cluster (e.g., in Sc3C2@ I h(7)-C80) can be readily controlled by exohedral radical addition, illuminating their future applications as single molecule magnets and in electronics. In addition, observation of the unexpected dimerization between two paramagnetic Y@ Cs(6)-C82 molecules suggests a spin-induced bonding behavior, which depends closely on the cage geometry. In contrast, synergistic effect of both electronic and geometric parameters has led to the formation of the unprecedented [6,6,6]-Lewis acid-base adduct of Sc3N@ I h(7)-C80. However, introduction of an oxygen atom gives rise to the corresponding normal carbene adducts for both Sc3N@ I h(7)-C80 and Lu3N@ I h(7)-C80, presenting an unexpected way of steric hindrance release. Remarkably, the Lewis acid-base complexation is demonstrated to be a facile way toward isomerically pure metallofullerene derivatives with surprisingly high regioselectivity and quantitative conversion yield for Sc2C2@ C3 v(8)-C82. This Account aims to give an advanced summary of the recent achievements in research of EMFs, focusing mainly on the interplay between the internal metallic species and the surrounding cages through bond formation or cleavage. Perspectives suggesting the future developments of EMFs are also given in the last section.