A novel phosphorus-containing, nitrogen-containing, and sulfur-containing reactive flame retardant (BPD) was successfully synthesized by 1-pot reaction. The intrinsic flame-retardant epoxy resins were prepared by blending different content of BPD with diglycidyl ether of bisphenol-A (DGEBA). Thermal stability, flame-retardant properties, and combustion behaviors of EP/BPD thermosets were investigated by differential scanning calorimetry (DSC), thermogravimetric analysis (TGA), limited oxygen index (LOI) measurement, UL94 vertical burning test, and cone calorimeter test. The flame-retardant mechanism of BPD was studied by TGA/infrared spectrometry (TGA-FTIR), pyrolysis-gas chromatography/mass spectrometry (Py-GC/MS), morphology, and chemical component analysis of the char residues. The results demonstrated that EP/BPD thermosets not only exhibited outstanding flame retardancy but also kept high glass transition temperature. EP/BPD-1.0 thermoset achieved LOI value of 39.1% and UL94 V-0 rating. In comparison to pure epoxy thermoset, the average of heat release rate (av-HRR), total heat release (THR), and total smoke release (TSR) of EP/BPD-1.0 thermoset were decreased by 35.8%, 36.5% and 16.5%, respectively. Although the phosphorus content of EP/BPD-0.75 thermoset was lower than that of EP/DOPO thermoset, EP/BPD-0.75 thermoset exhibited better flame retardancy than EP/DOPO thermoset. The significant improvement of flame retardancy of EP/BPD thermosets was ascribed to the blocking effect of phosphorus-rich intumescent char in condensed phase, and the quenching and diluting effects of abundant phosphorus-containing free radicals and nitrogen/sulfur-containing inert gases in gaseous phase. There was flame-retardant synergism between phosphorus, nitrogen, and sulfur of BPD.