Silicon carbide (SiC) is a material of great interest in many industrial applications. However, due to the hardness and brittleness nature, achieving ultra-precision machining of SiC is still challenging. In recent years, function surface with micro-structures has been introduced in cutting tool to suppress wear process. But the wear mechanism of the structured tool has not been revealed completely. Therefore, in present research, molecular dynamic simulations were conducted to investigate the influence of the micro-structure on the nano scale cutting process of 3C-SiC. The simulation results showed that the dislocation propagation in workpiece can be suppressed with a structured tool. The micro-structures have a great influence on the stress distribution in the workpiece subsurface. Furthermore, the abrasive wear of the structured tool is obvious smaller since the edges of the tool became blunt and the contact face between tool and workpiece changed to the close-packed plane of diamond. Moreover, the amorphization of the structured tool is effectively suppressed. This study contributes to the understanding of the details involved in the ultra-precision cutting of SiC.