The physical properties of modified nano-SiO₂ and methyl-phenyl-dimethoxy-silane modified phenolic resin are studied by molecular dynamics simulation. The results show that the glass transition temperature of unmodified phenolic resin at 300 K is 362 K, the elastic modulus and shear modulus are 5.45 GPa and 2.19 GPa, the thermal conductivity and thermal expansion coefficients are 0.37 W·(m·k)^-1 and 3.8×10^-5K^-1, respectively. The addition of nano-SiO₂ increases the glass transition temperature by 1.6%, the elastic modulus and shear modulus by 34.9% and 28.8%, and the thermal conductivity and thermal expansion by 11% and 31.6%, respectively. The thermal conductivity and thermal expansion are reduced by 11% and 31.6%, respectively. SiO₂ surface grafting 3%, 5%, 7% and 10% silane coupling agent and methyl-phenyl- dimethoxy-silane modified phenolic resin, the glass transition temperature increased by 10.5%, 15.2%, 16.8%, 19.3% and 1.5% respectively, the elastic modulus increased by 44.4%, 53.2%, 53.8%, 63.5% and 13.4% respectively, and the thermal conductivity decreased by 12.4%, 13.5%, 11.2%, 7% and 10% respectively. Moreover, the thermal expansion coefficient of phenol formaldehyde resin modified by methyl phenyl dimethoxy silane increased by 51.8% compared with the unmodified phenol formaldehyde resin. The study show that the doping of nano-SiO₂, the grafting of silane coupling agent on the SiO₂ surface, and the modification of methyl-phenyl-dimethoxy-silane can improve the glass transition temperature, and mechanical properties and reduce the thermal conductivity of phenolic resin. Only nano-SiO₂ doping can reduce the thermal expansion coefficient, whereas the modification of methyl-phenyl-dimethoxy-silane will increase substantially.