Epoxy resin nanocomposites reinforced with silica nanoparticles have been prepared at different nanoparticle loading levels. The surface functionality of the silica nanoparticles is manipulated by the phosphoric acid (H3PO4)-doped conductive polyaniline (PANI) via a surface initiated polymerization (SIP) method. The improved glass transition temperature (Tg) and enhanced mechanical properties of the cured epoxy resin nanocomposites filled with the functionalized silica nanoparticles are observed compared with those of the cured pure epoxy resin. The flammability and thermal stability behaviors of these nanocomposites are evaluated using microscale combustion calorimeter (MCC) and thermogravimetric analysis (TGA). The heat release rate (HRR) peak of the epoxy filled with functionalized silica nanoparticles is observed to decrease dramatically with increasing functionalized silica particle loadings, indicating a flame-retardant performance from the phosphoric acid-doped PANI.