The deposition processes for Al atoms on Pb (Al/Pb system) surface and Pb atoms on Al surface (Pb/Al system) are studied using molecular dynamic simulations. Under the same deposition conditions, the morphologies of the two systems are very different due to the difference in energy barrier between the interfaces. The substrate temperature, the atom incident energy, and the surface orientation are discussed in terms of their effects on the atom mixing between interfaces. The simulation results show that with the substrate temperature increasing, atomic mobility is enhanced and the degree of atoms mixing between interfaces becomes greater. However, the change of the atom incident energy has little effect on the atoms mixing between interfaces. The atoms mixing is obviously different due to the change of the surface orientation. The analysis on the pair correlation function g(r) indicates that the film formed with higher incident energy has a better quality. The radial distribution function in peak of the intermixing region reveals that a PbAl intermetallic compound may be formed at the interface between Pb and Al.