Pore deformation and damage are caused by the compression of the cutting tool during the machining of porous materials. Tool-edge radius is a key factor in the nano-cutting of pores and significantly influences the resulting deformation and damage. In this paper, the molecular dynamics simulations were conducted to investigate nano-cutting process of the non-continuous surface in single-crystal silicon. Surface morphology, pore wall deformation, cutting forces, and subsurface damage were calculated and discussed under different tool-edge radii. The results indicated that the change of the tool-edge radius greatly affect the machining quality of non-continuous surface. Cutting forces and accumulated material above the pores increase with increasing tool-edge radius, and the side of the tool entering the pore is more susceptible to damage than the opposite side. Additionally, normal force was identified as the primary cause of damage on the side of the tool entering the pore. The longitudinal damage depth on the side of the tool entering the pore increases with the tool-edge radius. Comprehensive analysis of material distribution, pore wall deformation and damage indicates that a smaller tool-edge radius is more conducive to pore processing.