To study the modification mechanism of graphene/rubber composite-modified asphalt, the blending system of graphene, rubber, and asphalt was studied by molecular dynamics simulation. The molecular models of asphalt, rubber asphalt, and graphene/rubber composite-modified asphalt were constructed by molecular dynamics software. The intermolecular binding energy, radial distribution function, and mechanical properties of the three asphalt systems were studied. The results showed that the addition of graphene increased the binding energy between rubber and light components of asphalt, promoted the absorption of light components of rubber, improved the binding stability of rubber and resin, and improved the compatibility of rubber and asphalt. Graphene can weaken the agglomeration behavior of asphaltene and rubber, and promote light components to penetrate and fill the agglomeration space between asphaltene, which improves the overall stability of the asphaltene system. Graphene promoted the swelling development of rubber and made rubber form a stable spatial grid structure in the asphalt, thus contributing to the elastic modulus, bulk modulus, and shear modulus of graphene/rubber and asphalt blending system compared to the matrix asphalt has a greater enhancement.