In order to study the influences of amino silane coupling agents with different grafting densities on the surface of nano silica on the thermomechanical properties of cross-linked epoxy resin, the molecular dynamics method was used to establish an amorphous model and calculate the mechanical properties, glass transition temperature, mean square displacement, hydrogen bond, binding energy, and radial distribution function of the composite models in this paper. The results are as follows: with the increase of the grafting density of an amino silane coupling agent on the surface of nano silica particles, the mechanical properties and glass transition temperature of epoxy resin showed a trend of increasing first and then decreasing. When the grafting ratio was 9%, the mechanical properties and glass transition temperature of the epoxy resin were the largest, and the glass transition temperature was increased by 41 K. At the same time, it was found that the higher the grafting ratio, the lower the chain movement ability, but the higher the binding energy. Besides, the binding energy between the nanoparticles of the grafted silane coupling agent and epoxy resin was negatively correlated with the temperature. By analyzing the hydrogen bond and radial distribution function, the results showed that the improvement of the grafted silane coupling agent on the surface of the nanoparticle to the thermomechanical properties of the epoxy resin was related to the OH···O and NH···O hydrogen bonds. The analysis results indicated that the proper grafting density should be selected based on the established model size, selected nanoparticle diameter, and epoxy resin materials in order to better improve the thermomechanical properties of the epoxy resin.