The combined effects of phosphorous-jointed epoxidized soybean oil and rice husk–based silica on the flammability and mechanical properties of epoxy resin were examined in detail. The chemical structures of the epoxidized soybean oil, phosphorous-jointed epoxidized soybean oil, and rice husk–based silica were confirmed using Fourier transform infrared spectroscopy and proton nuclear magnetic resonance. Many characteristics of the obtained composite materials were examined, such as the tensile properties, impact strength, flexural strength, critical stress intensity factor (KIC), dynamic mechanical analysis, and flammability. The incorporation of both 10 phr phosphorous-jointed epoxidized soybean oil and 20 phr rice husk–based silica into the epoxy resin yielded the optimum values of the flexural strength, tensile strength, impact strength, and KIC, with increases of 87.78%, 67.23%, 109.34%, and 111.32%, respectively, compared with pristine samples. The limiting oxygen index increased from 23.1% to 29.3%, the peak heat-release rate decreased by up to 37.2%, and the sample satisfied the UL94 V-0 rating.