A method for constructing the models of quartz glass was proposed to improve the processability of quartz glass, and Molecular Dynamics(MD) simulation combined with nano-indentation experiments were performed to research on nano-processing performance of the quartz glass. The accuracy of the model was verified by calculating the density and hardness of the quartz glass. Then the nano-indentation experiment was conducted to obtain indentation curves and to observe the morphology of indentation. Finally, a MD simulation of nano-indentation was performed and the formation and extending mechanism of a damage layer was investigated. According to the calculation of density and nano-hardness, it shows that the density is about 2.28 g/cm3 and nano-hardness is about 9.7—10.7 GPa, which is almost consistent with the experimental results. The experiments indicate that the quartz glass has a stable plastic deformation and a small amount of elastic deformation as well as the indentation size effect. When the indenter is depressed, the atomic dense area is formed. Since it losses the strength of the original covalent bonds, so the damaged layer is formed. Moreover, the surface topography is mainly formed by atoms on both sides squeezed with the indenter and the adhesion of the indenter. The simulation and experimental results show that the quartz glass is suitable for ultra-precision machining.