Large-scale molecular dynamics simulations of nanoindentation on a (100) oriented silicon surface were performed to investigate the mechanical behavior and phase transformation of single crystalline silicon. The direct crystalline-to-amorphous transformation is observed during the nanoindentation with a spherical indenter as long as the applied indentation strain or load is large enough. This amorphization is accompanied by a distinct discontinuity in the load–indentation strain curves, known as “pop-in”. Herein, we have demonstrated the pressure-induced amorphization processes via direct lattice distortion. Moreover, the combination of large shear stress and associated hydrostatic pressure facilitates this crystalline-to-amorphous transformation. The structural characteristics, phase distribution, and phase transformation path have also been discussed in this study. The present results provide a new insight into the mechanical behavior and phase transformation of monocrystalline silicon.