The molecular design concept of silicon-nitrogen synergistic effect for highly-efficient flame retardants has been demonstrated in the preparation of reactive type flame retardants which exhibits high flame retardation efficiency and property enhancement ability for developments of high performance polymers. In the synthetic route, a benzoxazine-containing triethoxysilane compound is obtained and used as a monomer together with diphenylsilanediol to result in branched benzoxazine-containing polysiloxanes (PBz-PSO) through a 3 + 2 condensation polymerization reaction. The chemical structures and properties of Bz-TES and PBz-PSO compounds have been characterized with Fourier transform infrared spectroscopy, nuclear magnetic resonance spectroscopy, and differential scanning calorimetry. PBz-PSO samples are reactive polymers as they possess thermally-reactive benzoxazine groups. Thermally-crosslinking the PBz-PSO samples results in silicon-containing polymers which show high thermal stability and high flame retardancy (limited oxygen index > 45). Addition of 5 wt% PBz-PSO to a conventional benzoxazine resin could simultaneously improve its flame retardancy (passing the UL 94-V0 test) and increase its glass transition temperature from 145 °C to 205 °C. PBz-PSO samples are highly-efficient reactive-type flame retardants for preparation of halogen-free and phosphorus-free polymers.