Aged asphalt mixture is heavily involved in pavement maintenance and renewed construction because of the development of recycling techniques. The aged bitumen binder has partially lost its viscous behavior. Rejuvenators are therefore designed and used in this recycling procedure to enhance the behavior of such aged reclaimed bitumen. However, tests have not yet been clearly specified to understand the diffusion characteristics of rejuvenators in aged bitumen. In this research, molecular dynamic simulation is proposed and conducted with Materials Studio software to study the diffusion behavior of rejuvenators in aged bitumen at the molecular level. Two rejuvenators, named R-1 and R-2, were included. The difference between these two rejuvenators is their chemical composition of C=O. The diffusion coefficient is determined by studying the molecular movement. Results illustrate that the proposed models can be used to study the diffusion of rejuvenators in aged bitumen sufficiently. In the meantime, a dynamic shear rheometer (DSR) is used to evaluate the recovery influence on aged bitumen resulting from rejuvenators. The experimental results strengthen the model simulations and indicate that the aging index of bitumen has a significant influence on the rejuvenating effect. Research results indicate that rejuvenators have a sufficient rejuvenating effect on the long-term aged bitumen and a limited effect on short-term aged bitumen.