To improve the mechanical properties of the rolling body surface of wind power bearings, extend its service life. In this study, a large-scale molecular/atomic parallel processor LAMMPS was introduced, and then the process of magnetron sputtering technology in the preparation of DLC/Ni-DLC thin films on the 42CrMo substrate material was simulated. The effects of deposition parameters such as sputtering temperature, sputtering voltage, deposition air pressure, and Ni doping on the residual stress, film base bonding, and organizational structure of the thin films were investigated. The simulation results were also verified experimentally by magnetron sputtering. The simulation results show that Ni doping and reasonable control of the deposition parameters can help reduce the residual stress and improve the bonding strength of the film by changing the film organization.