Sputtered Cu/Si thin films were experimentally prepared at different sputtering pressures and characterized using X-ray diffraction (XRD) and an atomic force microscope (AFM). Simultaneously, an application-oriented simulation approach for magnetron sputtering deposition was proposed in this work. In this integrated multiscale simulation, the sputtered atom transport was modeled using the Monte Carlo (MC) and molecular dynamics (MD) coupling method, and the deposition of sputtered atoms was simulated using the MD method. This application-oriented simulation approach was used to simulate the growth of Cu/Si(100) thin films at different sputtering pressures. The experimental results unveiled that, as the sputtering pressure decreased from 2 to 0.15 Pa, the surface roughness of Cu thin films gradually decreased; (111)-oriented grains were dominant in Cu thin films and the crystal quality of the Cu thin film was gradually improved. The simulation results were consistent with the experimental characterization results. The simulation results revealed that the transformation of the film growth mode from the Volmer–Weber growth mode to the two-dimensional layered growth mode resulted in a decrease in the surface roughness of Cu thin films; the increase in the amorphous compound CuSixand the hcp copper silicide with the decrease in the sputtering pressure was responsible for the improvement of the crystal quality of the Cu thin film. This work proposed a more realistic, integrated simulation scheme for magnetron sputtering deposition, providing theoretical guidance for the efficient preparation of high-quality sputtered films.