To Demonstrate the Rejuvenation Effect of Waste Soybean Oil (WSO) on Aged Asphalt Binder (AB) and Realise the Efficient Combination of Laboratory Evaluation and Numerical Simulation. the Rheological Properties and Molecular Dynamics Simulation of WSO Rejuvenated Binders Were Investigated. the Results Demonstrated that the WSO Provided Sufficient Light Components in the AB and Reduced the Stiffness. the WSO Rejuvenated Binders Were Transformed into a Sol–gel Structure, This Resulted in Excellent Rheological Properties. the WSO Improved the Anti-Fatigue Performance of Rejuvenated Binders. the WSO Provided Sufficient Aromatics and a Small Amount of Saturates for the AB. the Blending Mechanism of WSO and AB Was Physical Blending. the Atomic Force Microscopy Micromorphology Images Showed that the Bee-Like Structure of WSO Rejuvenated Binders Was Reduced in Quantity Compared with that of AB. the Dosages of 3–6 Wt% of AB Content Was Determined to Be the Optimum Content of WSO. the Molecular Dynamics Results Indicated that as the Amount of WSO Increased, the Total Volume and the Occupied Volume Increased, While the Free Volume Decreased. the Volume Fusion Parameters Increased Significantly with an Increase in the WSO Content. This Showed that WSO Effectively Improved the Diffusion Capacity of Rejuvenated Binders.