In recent years, the regeneration technology of aged asphalt in construction engineering has received much attention. The diffusion performance of the rejuvenator is a key factor in this kind of regeneration technology. But at present, the relevant research is still not mature. To forward this research, this study established molecular dynamic models of three diffusion systems with the open source large-scale atomic/molecular massively parallel simulator, including new asphalt, short-term aged asphalt and long-term aged asphalt. This study then analysed the diffusion mechanism and influence factors including temperature, ageing and the diffusion laws of different kinds of molecules. It was found that besides thermal motion, molecular force also greatly contributes to the diffusion of asphalt and rejuvenator. It was also found that micro voids in asphalt increase the contact area and promote the fusion of the rejuvenator and asphalt. Diffusion speed increases as temperature rises, and diffusion speed in aged asphalt is higher than that in new asphalt, especially at higher temperatures. The simulation results also suggest that small or catenarian molecules diffuse faster than the network structures.