In order to improve the hydrophobicity of waterborne flame retardant coatings, epoxy resin (EP) was used as coating material to encapsulate the flame retardants (ammonium polyphosphate, melamine and pentaerythritol) by single component modification and mixed component modification respectively. The surface groups of the flame retardant were analyzed by FTIR and the microstructure was observed by SEM. The contact angle of the flame retardant was measured and the particle size distribution was analyzed. The flame retardant and water-borne flame retardant coatings were tested by TG, respectively. The water resistance of the coatings was tested by the national standards GB/T 1733-93. The results show that: the flame retardants prepared by the two processes are coated with EP, and the optimum content of EP is 15wt%; with the decrease of the solubility of the flame retardants, the contact angle increases, and the water resistance of the waterborne flame retardant coatings is significantly improved; in addition, the flame retardant is more efficient by mixing components; The crosslinking of ammonium polyphosphate and EP results in unsaturated carbon-rich structure, which strengthens the stability of carbon skeleton and increases the quality of coating residues.