In the nanocutting process of graphene, the mechanism on the atomic scale of the effect of substrate hardness on the edge quality of graphene nanoribbons has not been thoroughly investigated. In this paper, we construct a diamond probe (radius of 5 Å) to cut graphene (190 Å × 113 Å) models with different substrates (silicon/sapphire/silicon carbide), molecular dynamics simulations were used to study the effect of substrate hardness and cutting depth on the atomic structure of graphene nanoribbon edges by observing the atomic morphology, the number of C-C bonds, the radial distribution function and friction. The results show that during the nanoindentation stage, when graphene is in the critical damage state, the substrate with high hardness has high deformation strength, the substrate deformation is small, and graphene undergoes deformation is also small, but the force Fz on the probe, the critical graphene stress σz and the equivalent stress are all large, and the number of C atoms with CN=3 is large; At the nano-cutting stage, the breakage of C-C bonds and the generation of edge defects are caused by local stress concentration, and the graphene stress σxx along the x-direction has a clear directionality. With the same cutting depth (critical damage depth of silicon substrate), silicon substrate hardness is small, the graphene nanoribbon obtained has less number of circular defects generated at the edge, less total number of defective atoms, more number of CN=3 atoms, large peak of radial distribution function of graphene after cutting, and graphene integrity is better. The hardness of the silicon carbide substrate is large, and the number of C-C bond breaks in graphene during the cutting process is high. Each substrate is cut at its own critical damage depth, and the substrate hardness has no significant effect on the number of C-C bond breaks, the number of circular defects, the total number of defective atoms, and the number of CN=3 atoms in graphene. When the silicon substrate was used, the stable force of the probe is small, the edge structure of graphene has little impact, the edge effect obtained is good. The cutting depth and substrate hardness have little effect on the graphene temperature during the nano-cutting process. In this paper, the atomic structure of graphene edges after cutting is analysed and investigated on the atomic scale, and the above results are combined to provide theoretical guidance for obtaining efficient and high-quality and low-damage graphene nanoribbon cutting.