Nano-particle reinforced polymer composites are widely applied in many fields because of good mechanical properties. In this paper, the cell model of SiO2/PI composite is built by the molecular dynamics simulation software Materials Studio, three processing methods are acted on the SiO2 nano-particle, -Si-C3H7 treatment, directly grafted with polyimide, covalently grafted with polyimide, effects of the modification methods on the mechanical properties of nano-particle reinforced polymer composites are studied. The mechanism of nano-particle surface modification effect on the composite is discussed through analyzing the potential change between the nano-particles and polymer matrix.