In industries like shipbuilding and aerospace, the ongoing need for advanced epoxy resins possessing superior mechanical strength and flame-retardant characteristics remains critical. In this study, a silicon-phosphorus blended resin (ED./EB) was synthesized using 10-(2,5-dihydroxy phenyl)-10-hydro-9-oxa-10-phosphaphenanthrene-10-oxide (DOPO-HQ) and hydroxyl-terminated silicone oligomer (Z-6018) as precursors. In comparison to epoxy resin (E−51), experimental results indicated a 16.7% increase in the tensile strength of ED/EB and a 20.7% increase in impact strength. The enhancement and toughening of the resin were simultaneously achieved through the silicon-phosphorus synergistic modification. The flame retardancy test indicates that ED./EB combines the outstanding smoke suppression of silicone modified resin (EB) with the high LOI of phosphorus modified resin (ED-27), while also decreasing the flame growth index (FIGRA) of the resin. After undergoing combustion, the silicon-phosphorus collaboration within the ED/EB material yielded a dense protective covering on the surface. This covering effectively governed the emission of smoke particles and heightened the residual mass. This work elucidates the impact of silicon-phosphorus synergy on the mechanical and flame-retardant properties of the resin, which is of great significance for developing high-performance resins.