In this study, a hierarchical multiscale homogenization procedure aimed at predicting the effective mechanical properties of silica/epoxy nanocomposites is presented. First, the mechanical properties of the amorphous silica nanoparticles are investigated by means of molecular dynamics (MD) simulations. At this stage, the MD modeling of three-axial tensile loading of amorphous silica is carried out to estimate the elastic properties. Second, the conventional twp phase homogenization techniques such as finite elements (FE), Mori-Tanaka (M-T), Voigt and Reuss methods are implemented to evaluate the overall mechanical properties of the silica/epoxy nanocomposite at different temperatures and at constant weight ratio of 5%. At this point, the mechanical properties of silica obtained in the first stage are used as the inputs of the reinforcing phase. Comparison of the FE and M-T results with the experimental results in a wide range of temperatures reveals fine agreement; however, the FE results are in better agreement with the experiments than those obtained by M-T approach. Additionally, the results predicted by FE and M-T methods are closer to the lower bound (Reuss), which is due to lowest surface to volume ratio of spherical particles.