A phosphorus-containing flame retardant monomer, bis(bisphenol A) monophenyl phosphonate (BPAMPP), was synthesized from bisphenol A (BPA) and benzene phosphorous oxydichloride (BPOD) and used as chain extender. A series of flame retardant waterborne polyurethanes (WPUP) with different mass fractions of BPAMPP were prepared by chain reaction of polyoxypropylene glycol (PPG) and isophorone diisocyanate (IPDI). The product BPAMPP was characterized by NMR and FTIR. The emulsion properties, mechanical properties, thermal properties and flame retardancy of WPUP were studied by particle size analysis, tensile test, TGA, limiting oxygen index test and cone calorimeter. The results showed that BPAMPP was successfully synthesized, and its char residue was 14.2% at 800℃. The WPUP emulsions had good particle size distribution and storage stability. When the mass fraction of BPAMPP was 8%, the prepared waterborne polyurethane film exhibited the best comprehensive performance. The tensile strength was 36.8 MPa, 5% weight loss temperature was 288.3℃, the limiting oxygen index (LOI), peak heat release rate (PHRR) and total heat of release (THR) were 26.8%, 631 kW/m2 and 76 MJ/m2, respectively.