Metal cluster fullerenes are a class of molecular nanomaterials with complex structures and novel properties. An in-depth study of their formation mechanism is a key topic for developing new high-yield synthesis methods and promoting the practical application of such molecular nanomaterials. To elucidate the formation mechanism of Sc3N@Cn, a representative sub-class of metal cluster fullerenes, this study developed a ReaxFF force field parameter set CNSc.ff using a single parameter optimization method and conducted systematic molecular dynamics simulations on a C-N-Sc mixed system using the newly developed force field parameter set. The results show that atomic nitrogen has strong attraction to both C and Sc atoms, and it plays a key role in the formation of Sc3N@Cn; the formation of Sc3N@Cn includes carbon cluster growth, Sc-based cluster growth and their encapsulation; temperature, carbon density, and atomic ratio all affect the relative yield of Sc3N@Cn; and the final products are a mixture of amorphous carbon, fullerenes, metallofullerenes, and metal cluster fullerenes. This study rationalizes the phenomena observed in the synthesis experiments and provides insights for the development of selective and high-yield synthesis methods for metal cluster fullerenes.