Monocrystalline silicon is prone to brittle fracture during the nano-cutting process. Surface modification through ion implantation to create an amorphous layer on monocrystalline silicon significantly enhances its processability. This paper conducted molecular dynamics simulations to deeply reveal the nanometric cutting mechanism for monocrystalline silicon with an amorphous layer. The influence of the amorphous layer on material removal, subsurface damage, cutting forces, stress distribution, and temperature profiles was analyzed and thoroughly discussed. The calculating results reveal that primary material removal mode transitions from shearing to extrusion under the influence of the amorphous layer. The presence of an amorphous layer can efficiently reduce stress concentration and defects in the nanometric machining process. When the thickness of the amorphous layer equals the cutting depth of the tool, subsurface damage is reduced to approximately 2 nm, indicating that an optimal surface quality is achieved. When the thickness of the amorphous layer reaches more than cutting depth, the hydrostatic stress of the monocrystalline silicon part is significantly lower than the phase transition threshold of 12 GPa, which greatly reduces the occurrence of phase transition. Furthermore, the formation and evolution of shear bands are the primary reasons for the fluctuations in cutting force. The cutting temperature is closely related to structural transformations. The heat generated by shear slip in monocrystalline silicon material is higher than the heat generated by plastic deformation of material in the amorphous layer. Moreover, the heat energy produced by plastic deformation of amorphous layer atoms exceeds that generated by structural transformation of monocrystalline silicon atoms. This work reveals the nanometric cutting behavior of the monocrystalline silicon material with amorphous layer surfaces based on phase transformation. It can provide effective references for the preparation of amorphous layer thickness and selection of cutting parameters in nanometric cutting process of the monocrystalline silicon with amorphous layer surfaces.