In this study, a comprehensive investigation on nano-scale indentation of monocrystal and polycrystalline silicon is carried out by adopting molecular dynamic (MD) simulation. Five levels of initial temperature (30K, 100K, 300K, 500K and 700K) are configured in this study and the simulation results reveal the amount of bct-5 silicon atoms at the maximum indentation position is not significantly affected by the initial temperature, substantially less ß-silicon atoms are observed with higher temperatures. The temperature effect on the unloading process is also discussed. Meanwhile, indentation force curves for polycrystalline silicon (grain size ranging from 6.45 nm to 20.48 nm) and single crystalline silicon is compared. The result shows that the normal Hall-Petch effect is not seen in the nano-indentation process of silicon. The grain boundary increases local stress during the indentation process and results in less formation of ß-silicon phase, but it hardly affects the formation of bct-5 silicon.