In this paper, the influence of tool shape on the surface quality of monocrystalline nickel nanofabrication is studied. The research mainly adopts the method of molecular dynamics simulation, through the statistics of the atomic coordinates of the machined surface, then calculates the influence of different tool rake angles on the surface roughness of monocrystalline nickel. It is concluded that the surface roughness distribution is ‘W’ when the rake angle of the diamond tool changes from −45° to +45°. When analyzing the relationship between the tool shape and the processing temperature, it is found that when the clearance angle of the tool reaches a certain range, the clearance angle is further increased, and the temperature of the workpiece does not change during machining. Therefore, a large number of simulations were carried out, and it was concluded that there is a critical clearance angle, and the critical clearance angle of the tool in the research conditions is 8–10°.