In this paper, we elucidate the filler effect of the vitrimer nanocomposites in the atomistic aspect for the first time with the molecular dynamics (MD) simulations. The self-healing properties are compared between GO/vitrimer nanocomposites and pristine vitrimers by the self-healing simulation containing the bond exchange reaction algorithm. The results reveal that GO reduces the vitrimers’ T g as well as the nanocomposites self-heal better than the vitrimers at all temperature ranges: temp. higher than T g of both, temp. between the two T g s, and temp. lower than T g of both. Atomistic investigations demonstrate that the number of new disulfide bonds that emerged during the self-healing simulation increases in GO/vitrimer nanocomposites, which corroborates adding GO into the vitrimer stimulates the bond exchange reaction. Moreover, our simulation results imply that diverse nanofillers can be adopted for the same purpose.