In this study, molecular dynamics (MD) simulation was used to investigate a new mechanical polishing method for three-body polishing of single crystal Si under the lubrication of graphene. The polishing depth and polishing speed were adjusted under the same processing parameters to compare the results. The development of polishing force, atomic displacement, coordination number, temperature, potential energy, friction coefficient, and polishing surface morphology was studied during nano-polishing. The analysis shows that the polishing depth in silicon polishing plays a crucial role in the change of coordination number of silicon. The deeper the polishing depth, the higher the polishing force, the more obvious the subsurface damage layer, the higher the potential energy. High defect atomic number and high normal stress. Moreover, the material removal rate is proportional to the polishing depth; a larger polishing speed significantly increases temperatures and potential energy. However, a smaller polishing rate does not result in fewer defective atoms and Bct5-SI/SI-II type atoms, as well as lower material removal efficiency. Finally, graphene-lubricated three-body polished single crystal silicon can improve the surface quality and reduce material removal efficiency.