In nanoscale ductile mode cutting of the monocrystalline silicon wafer, micro-, or nanogrooves on the diamond cutting tool flank face are often observed, which is beyond the understanding based on conventional cutting processes because the silicon workpiece material is monocrystalline and the hardness is lower than that of the diamond cutting tool at room temperature. In this study, the mechanism of the groove wear in nanoscale ductile mode cutting of monocrystalline silicon by diamond is investigated by molecular dynamics simulation of the cutting process. The results show that the temperature rise in the chip formation zone could soften the material at the flank face of the diamond cutting tool. Also, the high hydrostatic pressure in the chip formation region could result in the workpiece material phase transformation from monocrystalline to amorphous, in which the material interatomic bond length varies, yielding atom groups of much shorter bond lengths. Such atom groups could be many times harder than that of the original monocrystalline silicon and could act as “dynamic hard particles” in the material. Having the dynamic hard particles ploughing on the softened flank face of the diamond tool, the micro-/nanogrooves could be formed, yielding the micro-/nanogroove wear as observed.