The use of reclaimed asphalt pavement (RAP) is a hot research topic in the field of road engineering, as there are still many issues to overcome so as to become standard engineering applications. The diffusion of virgin/aged asphalt binder is a key process to improve RAP performance. In this study, the asphalt binder diffusion models were developed by molecular dynamics (MD) simulation. Two kinds of bio-rejuvenators (BR-1 and BR-5) were chosen to represent the straight-chain and aromatic structures, respectively. The method of relative concentration, radial distribution function (RDF), and microstructure morphology were used to evaluate the effect of bio-rejuvenators on the diffusion process of virgin/aged asphalt binder. The results showed that bio-rejuvenators had a positive effect on the fusion process between virgin and aged asphalt binder. The volume diffusion coefficient based on asphalt binder diffusion models indicated that the bio-rejuvenators accelerated the fusion process between the virgin and asphalt binder. After adding bio-rejuvenators to the aged asphalt binder, the agglomeration intensity in the SARA fractions was reduced to different degrees. Due to the aging of asphalt binder, asphaltenes formed different types of micro-stacking phenomena such as “T-shaped stacking,” “Face to Face stacking,” and “Offset Face to Face stacking.” The bio-rejuvenators of BR-1 and BR-5 exerted different regenerative effects during the diffusion process of aged asphalt binder. For BR-1, the “Pull-Out” and “Intercalation” effect can be observed in the process of asphaltene deagglomeration. “Pull-Out” is the main regenerative effect of BR-5 in aged asphalt binder. A strong electrostatic interaction occurs between BR-5 and PAHs in asphaltenes. Thus, BR-5 achieves the goal of aged asphalt binder regeneration by attracting PAHs.