The surface properties of coatings during deposition are strongly influenced by temperature, particle fluxes, and compositions. In addition, the precursor incident energy also affects the surface properties of coatings during sputtering. The atomistic processes associated with the microstructure of coatings and the surface morphological evolution during sputtering are difficult to observe. Thus, in the present study, molecular dynamics simulation was employed to investigate the surface properties of Au/Cu alloy coatings (Cu substrate sputtering by Au atoms) with different incident energies (0.15 eV, 0.3 eV, 0.6 eV). Subsequently, the sputtering depth of the Au atoms, the particle distribution of the Au/Cu alloy coating system, the radial distribution function of particles in the coatings, the mean square displacement of the Cu atoms in the substrate, and the roughness of the coatings were analyzed. Results showed that the crystal structure and the sputtering depth of Au atoms were hardly influenced by the incident energy, and the incident energy had little impact on the motion of deep-lying atoms in the substrate. However, higher incident energy resulted in higher surface temperature of coatings, and more Au atoms existed in the coherent interface. Moreover, it strengthened the motion of Cu atoms and reduced the surface roughness. Therefore, the crystal structure of coatings and the motions of deep-lying atoms in the substrate are not influenced by the incident energy. However, the increase in incident energy will enhance the combination of coatings and the base while optimizing the surface structure.