Nano-cutting causes internal microscopic defects in the workpiece, and this defect structure is closely related to the initial temperature of the cutting layer. In order to reduce the defects of workpieces in nano-cutting, a nano-cutting model of single-crystal copper with a cutting layer was constructed using molecular dynamics. Firstly, the applicable initial temperature of the cutting layer was determined by analyzing the changes in the structural volume and microscopic defects of the workpiece. Secondly, the effect of the initial temperature of the cutting layer on the cutting forces, dislocations and lattice was analyzed. Finally, the simulation results were indirectly verified by experiments. The results show that the applicable initial temperature range of cutting layer for single crystal copper is 293~400 K. As the initial temperature of the cutting layer increases, the transition rate of the lattice structure increases and the magnitude of the cutting force changes significantly, but the effect on fluctuations is small. When the initial temperature of the cutting layer is set in the range of 360~390 K, the surface microscopic defects of the single crystal copper workpiece are relatively less, and thus it is predicted that the surface quality of the single crystal copper workpiece is higher when it is machined in this initial temperature range.