This study employed molecular dynamics simulation to investigate the mechanism of action of graphene-modified asphalt. A series of molecular models of graphene-modified asphalt were constructed and validated using thermodynamic parameters. The impact of the graphene (PGR) size and number of layers on its interaction with asphalt components were examined, and the self-healing process and mechanism of action of PGR-modified asphalt were analyzed. The results demonstrated that the size and number of layers of PGR significantly influenced its interaction with asphalt components, with polar components demonstrating a stronger affinity for PGR. When the size and number of layers of PGR were held constant, the interfacial binding energy between it and ACR-modified asphalt was the highest, followed by SBS-modified asphalt, and 70# matrix asphalt exhibited the lowest interfacial binding strength. This interfacial binding strength is primarily attributed to intermolecular van der Waals interactions. Furthermore, the incorporation of multi-layer PGR can markedly enhance the mechanical properties of matrix asphalt, whereas small-sized PGR is more efficacious in improving the low-temperature performance of polymer-modified asphalt. PGR can act as a bridge between asphalt molecules through rapid heat transfer and π-π stacking with aromatic ring-containing substances, which markedly increases the free diffusion ability of asphalt molecules, shortens the healing time of asphalt, and enhances the collective self-healing performance of asphalt. This study provides an essential theoretical basis for understanding the mechanism and application of PGR in asphalt modification.