In nano-cutting, an element with uncertainty like cutting tool material can intensively affect the surface strength of manufactured materials during the plastic deformation progress. Via the method of molecular dynamics (MD) simulations, the interaction principle is studied in this article, considering three different cutting factors including cutting tool size, cutting angle, and cutting tool shape. Nano-crystalline (NC) Cu-Ag alloys with grain boundary affect zone (GBAZ) segregation are selected as the cutting workpiece. The outcomes indicate that the compression between the cutting tool and workpiece causes the formation of dislocations and chips. Using a larger cutting tool leads to a shorter time for misshapen nucleation and movement within the NC Cu-Ag alloy, more plastic deformation, and more average tangential forces. The cutting angle has a conspicuous effect on the dislocation domain and chip volume. Sharp tools can cause plastic deformation of the workpiece more easily. This study provides a theoretical basis for the design of nano-cutting workmanship to obtain suitable mechanical properties.