Silicone rubber composites doped with nanoparticles are widely used in the field of electrical and aerospace insulation. The silane coupling agent modified on the surface of the particles enhances the compatibility between the nanoparticles and the insulating material, thus further improving the mechanical, dielectric properties and thermal stability of the composites. On this basis, the silicone rubber composite system models of three silane coupling agents (KH550, KH560, KH570) modified SiO2 are established respectively. Through the analysis methods of interaction energy, free fraction volume, radial distribution function and pull-out simulation, the improving mechanism of three silane coupling agents modified SiO2 on material properties can be explored from the perspective of molecular simulation. The results show that the interaction energy between KH570/SiO2 and silicone rubber system is the largest regardless of temperatures (280K ~ 400K). At low temperature (280K), the free fraction volume of KH550 and KH560 modified SiO2 systems is lower than that of KH570 modified system, while at high temperature, the free fraction volume of KH570/SiO2 system is the lowest. The three silane coupling agents modified SiO2 all increase the Young's modulus and bulk modulus of silicone rubber composites, and reduced the relative dielectric constant of the composites. The silicone rubber composite system mixed with KH570/SiO2 has the largest adsorption capacity for water molecules and the most obvious effect to inhibit the diffusion of water molecule. The results of this work can provide reference for the design and performance optimization of modified SiO2/silicone rubber composites in hygrothermal environment.