Abstract This paper proposes a method that combines molecular dynamics with finite element deformation model (MDFM) to calculate the stress and strain of a single crystal nickel material that occur during the nano-scale cutting by concial tool. The flow stress–strain curve used in the MDFM model was obtained by nano-scale tension simulation using molecular dynamics method in this paper. Since the Young's modulus of the nano-scale single crystal nickel material is different from macroscopic scale. Therefore, the Young's modulus of the single crystal nickel material used in the MDFM model was obtained through a nano-indentation test under very low indentation loading. The MDFM only requires the elastic–plastic constitutive equation. The position and displacement components of atom in any temporary situation during nano-scale cutting could be found by using the 3D MD simulation. The atom is regarded as a node and the lattice is regarded as an element. The shape function concept of FEM is applied to calculate the strain of element from atom displacement. After simulation, it can be found that the accumulation behavior of cutting chip done by nano-cutting is quite similar to macroscopic cutting. This paper also finds that residual stress and residual strain will remain on the machined surface of single crystal nickel after cutting.