In recent years, nanomachining has received an increasing attention because of the remarkable advancement in sciences and technologies. In nanomachining process, the atomic interaction in surface and subsurface layers plays an important role. At such a small nanoscale, the traditional continuum representation method, such as finite element method, becomes questionable. This difficulty can be solved in general by molecular dynamics (MD). MD provides the necessary insight into nanomachining process and allows researching local material properties and behaviors in detail. Based on the large scale parallel algorithm, a new three–dimensional molecular dynamics simulation model was established for nanomachining of single crystal Cu. The interactions between workpiece atoms (Cu—Cu), copper and diamond atoms (Cu—C), and diamond atoms (C—C) were described by embedded atom method (EAM), Morse and Tersoff potentials, respectively. The temperature distribution and thermal effects during nanomachining were investigated. The chip formation and nanomachining mechanism were analyzed from the point of view of dislocation theory and thermal effects. The simulation results demonstrate that both the dislocation emission and chip pilep direction are along the h110i orientation. Temperature ditribution presents a roughly concentric shape and a steep temperature gradient lies in diamond tool, and the highest temperature is found in chip. The workpiece material becomes soft as the system temperature increases. Cutting speed and cutting edge radius have a significant effect on the system temperature distribution.