A novel type of microencapsulated ammonium polyphosphate (MAPP) with a triallyl cyanurate (TAC)/SiO2 double-layered shell was synthesized through in-situ polymerization, followed by the thiol-ene photograted reaction. With a double bond in the TAC outer shell, MAPP could be utilized as a highly efficient flame retardant for intumescent flame-retarded natural rubber (NR). The chemical structure, morphology, and performance of MAPP were characterized by X-ray photoelectron spectroscopy, Fourier-transform infrared spectroscopy, water contact angle (WCA), scanning electron microscopy, and thermogravimetric analysis. MAPP exhibited a hydrophobic feature with a WCA of 101 degrees because of its organic outer shell, which made MAPP well dispersed in the NR matrix as well as enhanced the compatibility between the MAPP and NR matrix. The resulting intumescent flame-retardant NR compounds not only achieved excellent flame-retardant performance but also obtain improved mechanical properties because of the presence of 3D-cross-linking networks between the MAPP and NR matrix. The NR/MAPP compounds also presented good water resistance because of the microencapsulation of APP with an SiO2 inner shell, which provided a waterproof barrier for APP. Based on the cone calorimetric results, the NR/MAPP compounds also presented a decline in total heat release and heat release rate but an improvement in ignition time due to the fact that both the SiO2 inner layer and TAC outer shell could enhance the formation of a high-strength thermally stable char layer during combustion, thus preventing heat transmission and diffusion. The significant enhancement in flame-retardant performance was principally ascribed to the synergistic char-forming effect derived from the APP core and TAC/SiO2 shell. This work provides a new idea for development of APP-based flame-retardant additives and also explores their potential applications in intumescent flame-retardant polymeric systems.