The molecular simulation method has been widely applied in various fields with the rapid development of computer technology. In this paper, the construction methods of the asphalt molecular model, modifier molecular model, aging asphalt model, aggregate model, as well as verification methods of the base asphalt model were summarized. Through the molecular dynamics (MD) simulation, the properties and performance of asphalt, the diffusion phenomenon of asphalt, the modifying effect of modifiers on asphalt, the aging and regeneration of asphalt and the interface interaction between asphalt and aggregates were discussed. The MD simulation method can forecast the characteristics of asphalt materials, such as the mechanical properties, low-temperature properties, anti-aging properties, self-healing properties of base asphalt, the compatibility between base asphalt and modifier, and the mechanical and adhesion properties of asphalt-aggregate interfaces, which bridged the gap between macroscopic and microscopic behaviors and offered a prescription for the widespread use of MD simulation. However, MD simulation in the asphalt system needed to be improved in areas such as model construction, force field optimization and model validation because the molecular dynamics simulation only focused on the physical interaction between asphalt materials and modifiers. Furthermore, the application of molecular dynamics in the asphalt mixture was currently only limited to the study of the interface between the asphalt and aggregates, and thus it was recommended to combine the finite element simulation and other simulation methods to investigate the asphalt mixture. The final part of the article provided an outlook on the future direction of MD simulation in asphalt systems. In the future, the MD method needed to be used to study the high-temperature rheological properties of asphalt, the simulation of the interface between asphalt and modifiers, and the interaction between various modifiers and asphalt. In addition, it was necessary to investigate the effect of multiple factors (such as crack width, modifier, temperature and rejuvenator) on the self-healing properties of asphalt. In order to investigate the chemical interactions between asphalt and modifiers, it was recommended to combine it with other simulation methods such as quantum mechanics. In the case of asphalt mixture, it was advised to combine it with simulation methods such as finite elements to study the properties of asphalt mixture.