In this work, the effects of 9,10-dihydro-9-oxa-10-phosphaphenanthrene-10-oxide (DOPO) grafted epoxidized soybean oil (ESO-G-DOPO) on mechanical properties and flame retardant of rice husk silica filled epoxy based composite were investigated detail. The silica was extracted from rice husk before using as reinforcement for epoxy resin. While the epoxidized soybean oil (ESO) was synthesized from soybean oil via epoxidation processing prior to react with 9,10-dihydro-9-oxa-10-phosphaphenanthrene-10-oxide (DOPO) to form ESO-G-DOPO. The Fourier transform infrared spectroscopy and nuclear magnetic resonance were used to confirm the chemical structure of silica, ESO and ESO-G-DOPO. The content of rice husk silica was also kept at constant of 20 wt.% while the content of ESO-G-DOPO was varying in range from 0 to 15 wt.% according to epoxy weight. The experimental results indicated that the presence of ESO-G-DOPO help to enhance the fracture energy, tensile strength, flexural strength up to 111.36, 67.26, and 87.79 %, respectively in comparison with virgin sample. Especially, the results of cone calorimeter testing, limiting oxygen index indicated that the flammability of epoxy resin was extremely reduced with presence of ESO-G-DOPO. A mechanism of flame retardant was also proposed to answer for the question how ESO-G-DOPO acted in a flame.