Plenty of research has verified that nano-ZnO particles could improve the properties of asphalt, but studies on nano-ZnO-modified asphalt haven’t been conducted at the molecular level. Therefore, to investigate the effect of ZnO particles on the properties, structure and morphology of asphalt, the molecular dynamics (MD) methods were carried out. In this study, the models of asphalt, ZnO cluster and ZnO/asphalt blending systems with different particle sizes were built using Materials Studio software. Then, the interaction energies of ZnO/asphalt blending systems under different temperatures were calculated, and the effect of ZnO particles on the modulus and glass transition temperature of matrix asphalt was simulated. The results indicated that the bulk modulus of asphalt increased by ZnO with particle size at 4 Å, 6 Å, 8 Å and 10 Å increased by 15.09%, 12.46%, 10.06% and 8.51%, respectively, which can illustrate that the shear resistance ability and low-temperature properties of asphalt were enhanced. Compared with matrix asphalt, the glass transition temperature of the ZnO/asphalt system decreased by less than 0.1 K, indicating that ZnO’s effect on the low temperature of asphalt was not apparent. With the increase of ZnO particle size, the diffusion coefficient decreased sharply. Compared to matrix asphalt, when the particle size increased to 8 Å and 10 Å, the diffusion coefficient decreased by 13% and 22%, respectively. So, in practice projects, to achieve better dispersion of particle materials in base bitumen, a smaller particle size would be recommended. The results of the radial distribution function (RDF) and AFM simulation indicated that ZnO particles changed the micro-structure of asphalt and increased the roughness of the asphalt surface. As a result, ZnO particles bring matrix asphalt better physical properties.