During cancer development, the fibrous layers surrounding the tumor surface get thin and stiff which facilitates the tumor metastasis. After the treatment of metallofullerene derivatives Gd@C82(OH)22, the fibrous layers become thicker and softer, the metastasis of tumor is then largely suppressed. The effect of Gd@C82(OH)22 was found to be related to their direct interaction with collagen and the resulting impact on the structure of collagen fibrils, the major component of extracellular matrices. In this work we study the interaction of Gd@C82(OH)22 with collagen by molecular dynamics simulations. We find that Gd@C82(OH)22 can enhance the rigidity of the native structure of collagen molecules and promote the formation of an oligomer or a microfibril. The interaction with Gd@C82(OH)22 may regulate further the assembly of collagen fibrils and change the biophysical properties of collagen. The control run with fullerene derivatives C60(OH)24 also indicates that C60(OH)24 can influence the structure and assembly of collagen molecules as well, but to a lesser degree. Both fullerene derivatives can form hydrogen bonds with multiple collagen molecules acting as a “fullerenol-mediated bridge” that enhance the interaction within or among collagen molecules. Compared to C60(OH)24, the interaction of Gd@C82(OH)22 with collagen is stronger, resulting in particular biomedical effects for regulating the biophysical properties of collagen fibrils.