In order to better understand the mechanisms of tungsten (W) film delamination from the silicon (Si) substrate, a three-dimensional molecular dynamics (MD) simulation is being conducted to investigate the formation of residual stress during the film deposition process. For the purpose of simplicity, a Morse pair potential is proposed in this paper to simulate the interactions between W and Si atoms during the film deposition process. It appears from numerical solutions that the residual stress field in the W film is very sensitive to the W–Si interfacial potential model proposed for the MD simulation. By calibrating the controlling parameters in the interfacial potential model using the comparison between the simulated stresses and experimental data, the film stress transition from tension to compression during the film deposition process could be qualitatively simulated via the proposed simulation procedure. The numerical results presented in this paper provide a better insight into the effect of interfacial atomic potential on the stress transition in thin films. In addition, it can be seen from the MD simulation that there might exist a phase transition from the crystalline Si to amorphous W–Si structure to crystalline W around the interface area. Well-designed experiments are required to verify the simulation results.