In this paper, the molecular dynamics method is used to study the tool wear of nanotwinned cBN (nt-cBN) tool during nano-cutting of Nickel-based superalloys. It is determined that the main wear mechanism of the nt-cBN tool in the cutting process is diffusion wear. In the region where tool diffusion wear occurs, the phenomenon of nt-cBN tools changing from zinc amphibole cBN SP3 hybridization to layered hBN SP2 hybridization occurs. The workpiece atoms that diffuse into the tool act as metal catalyst atoms to achieve the transfer of electrons from the SP3 hybridized B atom to the N atom, realizing the transition from SP3 hybridization to SP2 hybridization. This structural transformation affects the performance of the tool, resulting in lower tool strength and more diffuse wear phenomena. Diffused workpiece atoms make the tool lattice distort and lead to the generation of tensile stresses in the tool cutting edge, which can promote the occurrence of tool diffusion wear and provide favorable conditions for structural phase transformation of the tool. Tool temperature and diffusion wear interact. The high cutting temperatures leads to more severe diffuse wear and diffusion wear affects tool thermal conductivity. Diffusion wear occurs in areas where high temperatures are concentrated and makes tool wear worse.