The deposition process for Be atoms on Be substrate is studied using molecular dynamic simulations. The morphologies of the deposited films are distinctly different under different incident energies. In a specified range, the surface roughness of the film decreases with the increase of the incident energy. However, the over-high incident energy is unfavourable for reducing the surface roughness of the film. The distributions of the coordination numbers and potential energy of the single atom are used to analyze the film structure under different incident energies. With the bigger incident energy the density of the film is bigger and the distribution of the potential energy of the single atom is more continuous. At the same time, the distribution of the atomic stress is more continuous. Finally, the energy conversion process of the single atom is given, and the influence of the initial incident energy on the locally accelerated energy near the substrate is analyzed.