To comprehensively understand the impact of various environmental factors on the self-healing process of graphene-modified asphalt, this study employs molecular dynamics simulation methods to investigate the effects of aging degree (unaged, short-term aged, long-term aged), asphalt type (base asphalt, graphene-modified asphalt), healing temperature (20 °C, 25 °C, 30 °C), and damage degree (5 Å, 10 Å, 15 Å) on the self-healing performance of asphalt. The validity of the established asphalt molecular models was verified based on four physical quantities: density, radial distribution function analysis, glass transition temperature, and cohesive energy density. The simulated healing time for the asphalt crack model was set to 200 ps. The following conclusions were drawn based on the changes in density, mean square displacement, and diffusion coefficient during the simulated healing process under different influencing factors: Dehydrogenation and oxidation of asphalt molecules during the aging process hinder molecular migration within the asphalt crack model, resulting in poorer self-healing performance. As the service life increases, the decline in the healing performance of graphene-modified asphalt is slower than that of base asphalt, indicating that graphene-modified asphalt has stronger anti-aging properties. When the vacuum layer in the asphalt crack model is small, the changes in the diffusion coefficient are less pronounced. As the crack width increases, the influence of various factors on the diffusion coefficient of the asphalt crack model becomes more significant. When the crack width is large, the self-healing effect of asphalt is more dependent on these influencing factors. Damage degree and oxidative aging have a more significant impact on the healing ability of graphene-modified asphalt than healing temperature.