Ammonium polyphosphate (APP), a widely used intumescent flame retardant, has been microencapsulated by cellulose acetate butyrate with the aim of enhancing the water resistance of APP and the compatibility between the ethylene-vinyl acetate copolymer (EVA) matrix and APP. The structure of microencapsulated ammonium polyphosphate (MCAPP) was characterized by Fourier transform infrared spectroscopy (FTIR), X-ray photoelectron spectroscopy (XPS), scanning electron microscopy (SEM), and water contact angle (WCA). The flame retadancy and thermal stability were investigated by a limiting oxygen index (LOI) test, UL-94 test, cone calorimeter, and thermogravimetric analysis (TGA). The WCA results indicated that MCAPP has excellent water resistance and hydrophobicity. The results demonstrated that MCAPP enhanced interfacial adhesion, mechanical, electrical, and thermal stability of the EVA/MCAPP/polyamide-6 (PA-6) system. The microencapsulation not only imparted EVA/MCAPP/PA-6 with a higher LOI value and UL-94 rating but also could significantly improve the fire safety. Furthermore, the microencapsulated EVA/MCAPP/PA-6 composites can still pass the UL-94 V-0 rating after treatment with water for 3 days at 70 °C, indicating excellent water resistance. This investigation provides a promising formulation for the intumescent flame retardant EVA with excellent properties.