In this study, molecular dynamics simulations have been used to investigate the effects of organic/inorganic components on the properties of silica nanoparticle/hydroxyapatite fiber reinforced Bis-GMA/TEGDMA dental composite materials. Characterization at the atomic scale is highly important for an advancement of the understanding of properties of resin based materials. Various combinations of Bis-GMA/TEGDMA (20–80% by weight) were modelled using molecular dynamics. The silica nanoparticle weight percentage was varied from 0 to 11% and the hydroxyapatite fiber weight percentage was varied from 0 to 12%. It was observed that the radius of gyration, in various blends of resin, lie in the range of 16–17 Å and thus was approximately independent of Bis-GMA/TEGDMA weight percentage. It was found that a small percentage of silica nanoparticle improved the mechanical properties significantly because of an increase in the volumetric hydrogen bonds and polymer chain contraction. As the weight percentage of TEGDMA in dental resin blends was increased from 20 to 80%, the hydrogen bonds per unit volume were found to decrease from 1.3 × 10−3 to 0.3 × 10−3 Å−3. The elastic and shear moduli of dental composites containing varying percentage of hydroxyapatite fibers (0–12%) increased by 8.13 and 10% respectively. In comparison to the hydroxyapatite fibers, the silica nanoparticles provided significant mechanical reinforcement effect. The diffusion coefficient falls approximately by 46%, from 1.15 × 10−11 to 0.62 × 10−11 m2/s with an increase in the silica nanoparticle weight percentage from 0 to 11 %. This indicated a strong dependency on change in chain conformation as well as hydrogen bonds. These findings will be of great importance in improving the understanding of the mechanical and dynamic properties of dental materials at the atomic/nanoscale.