Molecular dynamics model of monocrystalline silicon nanoindentation in the micro-nano-scale is established based on molecular dynamics theory. The deformation mechanism, potential energy change and temperature change of monocrystalline silicon is studied in the simulation process. Study found: The dislocation, vacancies and slip bands are observed on the substrate, there is projection phenomenon on both sides of substrate. When the indenter is evacuated, there is a phenomenon of necking between the substrate and the indenter. At the same time, the study found that the potential energy of the system is different when the system is in equilibrium, because the dislocation movement makes the system increased potential energy less than the work done by the indenter. The change of temperature is associated with the degree of dislocation deformation and the system temperature rises faster with intensity of dislocation deformation.