The invention discloses intrinsic type halogen-free flame retardant vinyl ester resin and a preparation method thereof. The resin is intrinsic type halogen-free flame retardant vinyl ester resin containing elements P and N. The preparation method of the resin comprises the following steps: (1) adding 1 weight part of TGIC (triglycidyl isocyanurate), 3 to 3.15 weight parts of unsaturated monocarboxylic acid and 0.3 weight percent of a polymerization inhibitor into a three-neck flask, stirring the components at a constant speed, heating the components to be at 80 to 85 DEG C, and when reactants are dissolved and colorless transparent liquid is formed, adding 0.5 weight percent of a catalyst for reaction at 110 to 115 DEG C for 3.5 hours; (2) adding 0.9 to 1.16 weight parts of DOPO, quickly stirring the DOPO, preserving the temperature for 4 hours, so as to obtainflame retardant vinyl ester TGIC-AA-DOPO; (3) cooling the flame retardant vinyl ester TGIC-AA-DOPO to 80 to 90 DEG C, adding a diluent, performing quick refluxing and stirring for 0.5 hour, and discharging a material. The resin is obvious in flame retarding effect, and maintains high process and physical mechanical properties, solves the technical problems of low process property and stability of adding type flame retardant vinyl ester resin and non environmental protection due to introduction of a halogen element by chemical reaction type flame retardant vinyl ester resin, and can be applied to the field of chemical engineering, environmental protection, housing construction, aerospace and the like.