When water interacts with bitumen, the diffusion and cohesion characteristics between the components of bitumen are negatively impacted. Molecular dynamics simulations were employed to construct various bitumen models, including bitumen–bitumen (without water), water-containing single bitumen, water-containing bitumen–bitumen, and bitumen–water–bitumen models. The primary research objectives were as follows: comparing the changes in the densities of bitumen models with and without water, analyzing the interlayer cohesive energies of bitumen models interacting with water, evaluating the hydrogen bonds in water-containing bitumen models, and characterizing the diffusion behaviors of bitumen components. The results indicated that when water interacted with the bitumen, it filled internal voids, leading to an overall increase in volume and reduction in density. The interaction energies between the rejuvenated bitumen models and water molecules decreased as the numbers of polar sites exposed to SBS molecules decreased. The numbers of hydrogen bonds between water molecules and rejuvenated bitumen models were similar to those in aged bitumen models. As the number of fractured SBS molecular chains gradually increased, the interlayer cohesive energy in the Methylene-bis(4-cyclohexylisocyanate) (HMDI)-rejuvenated bitumen model gradually increased. Water molecules significantly influenced the interactions at the rejuvenated bitumen–rejuvenated bitumen interface, weakening the cohesion characteristics between bitumen molecules. Water interactions significantly reduced the interlayer cohesive energy of the bitumen–water–bitumen model. Conversely, the recovery process improved the interlayer cohesion characteristics of the bitumen. The diffusion characteristics of the components of bitumen SARA were significantly greater under wet conditions than under dry conditions.