This paper aims to study the interaction mechanism of waste tire/plastic modified asphalt from the microscopic perspective of molecules. Based on BIOVIA Materials Studio, a classic four-component asphalt model consisting of asphaltene (C149H177N3O2S2), resin (C59H85NOS), aromatic (C46H50S), and saturate (C22H46) was constructed. Waste tires are represented by natural rubber (NR), which uses cis-1, 4-polyisoprene as a repeating unit. In contrast, waste plastics are characterized by polyethylene (PE), whose optimum degree of polymerization is determined by the difference in solubility parameters. Then, the above molecular models are changed to a stable equilibrium state through the molecular dynamics process. Finally, the interaction process is analyzed and inferred using the indexes of radial distribution function, diffusion coefficient, and concentration distribution; further, the interaction mechanism is revealed. The results show that the optimal degree of polymerization of PE is 12, so the solubility parameter between PE and NR-modified asphalt is the lowest at 0.14 (J/cm3) 1/2. These models are in agreement with the characteristics of amorphous materials with the structures ordered in the short-range and long-range disordered. For NR-modified asphalt, the saturate moves fastest, and its diffusion coefficient reaches 0.0201, followed by that of the aromatic (0.0039). However, the molecule of NR ranks the slowest in the NR-modified asphalt. After the addition of PE, the diffusion coefficient of resin increased most significantly from 0.0020 to 0.0127. NR, PE, and asphaltene have a particular attraction with the lightweight components, thus changing to a more stable spatial structure. Therefore, using NR and PE-modified asphalt can change the interaction between asphalt molecules to form a more stable system. This method not only reduces the large waste disposal task but also provides a reference for the application of polymer materials in modified asphalt.