Silicon carbide (SiC) is being increasingly applied in several engineering fields owing to its excellent mechanical and electrical properties. Although much attention has been paid to the material removal mechanism of SiC, producing an efficiently machined SiC surface with a high-quality surface and low-damage subsurface is still a challenging issue. Therefore, there is a need to investigate the material removal mechanism of SiC and explore the appropriate technical parameters for improving the processing performance. In this study, the effect of ion implantation on the material removal mechanism of single-crystal 6H-SiC is investigated numerically using molecular dynamics (MD) simulation. Forty-five silicon atoms were implanted into 6H-SiC individually. The lattice damage and hydrostatic pressure were analysed in detail. Then, nano-cutting simulations were carried out to machine both the 6H-SiC and implanted SiC using a diamond tool. The effect of ion implantation on the ductile deformation, minimum cutting thickness (MCT), and cutting force were determined. The results of this study demonstrate that ion implantation effectively increases MCT and decreases the cutting force, thereby improving the machinability and processing efficiency of 6H-SiC. This study has significant theoretical and practical value in processing technology.