This study utilized molecular dynamics simulation to investigate the adhesion process between wood tar-rejuvenated asphalt and acid/alkaline aggregate. Initially, various indicators including the contact area, cohesion coefficient, and interaction energy were employed to assess the adhesion effect under dry conditions. This revealed the action mechanism of the wood tar-rejuvenator in enhancing the adhesion performance between aged asphalt and aggregate. Subsequently, an asphalt–water–aggregate interface model was developed to simulate the water damage process of the asphalt mixture. This aimed to unveil the damage mechanism of water intrusion on the adhesion performance of the asphalt–aggregate interface and evaluate the water damage resistance of wood tar-rejuvenated asphalt through adhesion energy, stripping work, and the energy ratio. The findings indicate that wood tar-rejuvenated asphalt exhibits favorable adhesion properties with both acid and alkaline aggregates. The addition of wood tar-rejuvenated asphalt increased the interaction energy between aged asphalt and acid and alkali aggregates by 67.75 kJ/mol and 97.3 kJ/mol, respectively. The addition of a wood tar rejuvenator enhances the interaction energy between aged asphalt and aggregate, thereby increasing mutual attraction and enlarging the contact area. The adhesion between asphalt and aggregates hinges on the interaction between asphaltene and aggregates, and the wood tar rejuvenator reduces the diffusion ability of asphaltene in the attractive state of the aggregate, resulting in stable aggregation. Moisture intrusion increased the aggregation distance between asphaltene and aggregate by 14.1% and decreased the degree of aggregation by 24.0%, thereby reducing the interaction energy. The extent of damage caused by water intrusion is linked to the aggregation distance, with greater distances leading to deeper damage. Under wet conditions, the interaction energy of wood tar-rejuvenated asphalt increased by 78.2% in the acidic aggregate system and 98.1% in the basic aggregate system compared with aged asphalt. Meanwhile, wood tar-based rejuvenated asphalt improves the adhesion between aged asphalt and aggregate and reduces the stripping function of asphalt affected by water replacement, which results in the ER value of wood tar-rejuvenated asphalt being higher than that of the original asphalt by 0.12 and 0.22 in the acidic and alkaline environments, respectively, thus showing excellent resistance to water damage. This study provides new criteria for the selection of rejuvenators for waste asphalt, which will help in the future selection of superior rejuvenators for aged asphalt and reduce the possibility of choosing the wrong rejuvenator.