This paper explores the evolution mechanisms of metastable phases during the nanoindentation on monocrystalline silicon. Both the molecular dynamics (MD) and the in situ scanning spreading resistance microscopy (SSRM) analyses were carried out on Si(100) orientation, and for the first time, experimental verification was achieved quantitatively at the same nanoscopic scale. It was found that under equivalent indentation loads, the MD prediction agrees extremely well with the result experimentally measured using SSRM, in terms of the depth of the residual indentation marks and the onset, evolution and dimension variation of the metastable phases, such as beta-Sn. A new six-coordinated silicon phase, Si-XIII, transformed directly from Si-I was discovered. The investigation showed that there is a critical size of contact between the indenter and silicon, beyond which a crystal particle of distorted diamond structure will emerge in between the indenter and the amorphous phase upon unloading.