Abstract: Silicon (Si) plays an irreplaceable role in large scale integrated circuit, micro/nanoelectromechanical systems (MEMS/NEMS), and semiconductor industry. Its nanomechanical behavior and pressure phase transformation are always of immense interest and have been a focus of extensive experimental and theoretical researches for a few decades. We performed a large-scale molecular dynamics simulation of the nanoindentation on Si(100) surface to examine the nano-mechanical behavior and phase transformation mechanism of monocrystalline silicon. In the simulations, a large indenter with radius of ~21.73nm was utilized in order to approach the experimental indenter size. Benefit from the large indenter, the detailed phase transformation process and phase distribution were analyzed, and the structure of the high pressure phase was characterized by radial distribution function (RDF) and bond angle distribution function (ADF). The results showed that the load-depth curve in elastic stage was agreed well with the prediction of the Hertz contact theory. The mismatch between simulated load-depth curve and Hertz contact accurately indicated the onset of plastic deformation, which was corresponding with the initial phase transition from Si-I phase with diamond structure to bct5 phase with body-centered cubic (bcc). The initial bct5 phase generated an inverted pyramid on the subsurface. Increasing the indentation load, the Si-II phase was generated from the Si-I phase, and enlarged beneath the indenter. The bct5 phase formed a fourfold pattern along the indentation orientation. Compared with the small indenter, the large indenter prompted the grown of the Si-II phase, which is the one reason why the BCT5 phase almost cannot be probed in experiment. After unloading, both the Si-II and bct5 phases transformed into amorphous phase. The results validated the existence of bct5 in the nano-indentation process of monocrystal silicon; and revealed the phase transformation mechanism of the plastic deformation.