In this paper, a molecular dynamics simulation method was used to study the thermo-mechanical properties of cross-linked epoxy resins doped with nano silica particles that were grafted with 3-aminopropyltriethoxysilane, N-(2-aminoethyl)-3-aminopropyltrimethoxysilane, and 3-[2-(2-aminoethylamino)ethylamino]-propyl-trimethoxysilane with different chain lengths. Firstly, a set of pure epoxy resin models, and four sets of SiO2/EP composite models were established. Then, a reasonable structure was obtained through a series of optimizations using molecular dynamics calculations. Next, the mechanical properties, hydrogen bond statistics, glass transition temperature, free volume fraction, and chain spacing of the five models were studied comparatively. The results show that doped nano silica particles of surfaces grafted with 3-aminopropyltriethoxysilane, N-(2-aminoethyl)-3-aminopropyltrimethoxysilane, and 3-[2-(2-aminoethylamino)ethylamino]-propyl-trimethoxysilane with different chain lengths enhanced mechanical properties such as elastic modulus, shear modulus, and volume modulus obviously. The glass transition temperature increased by 15–16 K, 40–41 K, and 24–27 K, respectively. Finally, the data show that the cross-linked epoxy resin modified by nanoparticles grafted with N-(2-aminoethyl)-3-aminopropyl trimethoxysilane had better effects for improving thermo-mechanical properties by the comparatively studying the five groups of parameter models under the same conditions.