Epoxy resin (EP) has excellent comprehensive properties, but its inherent flammability limits its further application in high‐end industries. The present study focuses on the preparation of an efficient phosphorus/silicon‐containing flame retardant for improving the flame retardancy and smoke suppression of EP. The intermediate product ED was first obtained by the addition reaction of 9,10‐dihydro‐9‐oxa‐10‐phosphaphenanthrene‐10‐oxide (DOPO) with eugenol, and then the target flame retardant DPSi‐ED was synthesized by the Williamson etherification reaction between ED and dichlorodiphenylsilane. The flame retardant was further incorporated into EP/4,4′‐diaminodiphenylmethane (DDM) system to prepare the modified epoxy thermosets. The flame‐retardant performance and mechanism were investigated by limiting oxygen index (LOI) test, vertical combustion test, cone calorimetry, thermogravimetric analysis‐infrared spectroscopy (TG‐IR), and so forth. At the same phosphorus content (0.5 wt%), EP/DPSi‐ED thermosets exhibited superior flame‐retardant properties to EP/ED thermosets. Moreover, EP/DPSi‐ED7 achieved a LOI of 35.3% and V‐0 rating in UL‐94 testing, and compared to EP/ED7, its peak heat release rate (pHRR) and total smoke production (TSP) were reduced by 31.5% and 10.9%, respectively. The phosphorus and silicon elements synergistically contributed to the formation of a stable char layer, which acted as a physical barrier to effectively enhance the flame‐retardant properties of the thermosets. Meanwhile, the incorporation of DPSi‐ED containing flexible SiO bonds and rigid DOPO groups to some extent also improved the mechanical properties of the cured EP. Hence, this study provides an effective strategy for the preparation of bio‐based phosphorus/silica‐containing high‐efficiency and smoke‐suppressing flame retardants.