This paper explores the effect of the depth-of-cut of an indenter on the phase transformations during nanoscratching on monocrystalline silicon on the Si(100) orientation. The analysis was carried out by molecular dynamics simulations. It was found that the depth-of-cut and the impingement direction of the indenter had a significant influence on the phase transformations in the initial impression region. At a relatively low depth-of-cut, only amorphous silicon was formed on the scratched surface. When the indenter impinged on a silicon surface with an angle, a bct5-Si crystalline phase in the initial impression region would emerge.