Piperazine pyrophosphate (PAPP) combined with melamine polyphosphate (MPP) was adopted to prepare a waterborne fire retardant intumescent coating (IC) for structural steel. Silicone acrylic emulsion was used as binder. In the 2-h torch test, PAPP/MPP-IC coating presented excellent fire resistance performance. The equilibrium temperature at the backside of the steel board decreased to 170 °C with protection of MPP/PAPP-IC, compared with 326 °C of APP/PER/MEL-IC. After 72-h water immersion, MPP/PAPP-IC could still provide sufficient thermal isolation, but APP/PER/MEL-IC failed the test. The water absorption of the MPP/PAPP coating was also reduced. The thermogravimetric analysis measured that the PAPP/MPP-IC had unique initial decomposition temperature of 296 °C and higher residue of 33.8 wt%, which demonstrated better thermal stability and fire retardancy in condensed phase. In addition, Scanning Electron Microscope (SEM) images illustrated that the structure of the carbon layer formed by MPP/PAPP-IC was dense, complete and consistent, indicating the improvement of mechanical strength and thermal isolation of the char. The synergistic effect between piperazine and phosphoric acid groups in MPP/PAPP contributed to the superior flame retardancy. Consequently, MPP/PAPP-IC was much more efficient than the traditional APP/PER/MEL-IC. This work provides a novel way for designing flame retardant coatings for structural steel with excellent comprehensive performance.