A unique hybridized intumescent flame retardant (hIFR), of which expandable graphite (EG) is chemically coated by organic chains containing phosphorous and nitrogen elements, was synthesized and characterized. Based on the successful synthesis, hIFR was used to develop modified cyanate ester (CE) resins with super flame retardancy. With the addition of only 5 wt% hIFR into CE resin, the peak and total heat releases significantly reduce to values that are only 32.3 and 23.1% of that of CE resin, respectively; meanwhile the fire performance index and limited oxygen index increase about 2 and 1.4 times. Besides, both smoke and carbon monoxide releases are remarkably reduced. These attractive data are much better than those of the modified CE resin with 5 wt% EG, clearly demonstrating that hIFR is a super flame retardant. Besides the traditional investigations on the structures of chars and cone calorimeter tests, an intensive study on the thermodegradation kinetics was carried out to reveal the mechanism of the outstanding flame retarding performance of the hIFR/CE resins. Different from EG, the unique structure of hIFR provides multi-effects on improving the flame retardancy, they are taking part in the structural formation of a cured network, increasing the thermal stability during the whole process of degradation, and strengthening the ability to form a thermally stable and condensed barrier for heat and mass transfer. These attractive features of hIFR/CE resins suggest that the method proposed herein is a new approach to prepare very effective flame retardants and corresponding super flame retarding resins.