The invention provides a preparation method of a fluorine modified epoxy phosphate water dispersion. The preparation method comprises following steps: 1, epoxy resin, a small molecular alcohol, a first catalyst, and an alcohol ether solvent are introduced into a reaction container for mixing heating, isocyanate is added, an obtained mixture is heated slowly, a second catalyst is added for reactionuntil the epoxide equivalent of the epoxy resin ranges from 252 to 340; 2, the alcohol ether solvent is added for cooling, bisphenol A, hydrogenated bisphenol A, bisphenol AF, and the second catalystare added, the temperature is increased to 140 to 160 DEG C with stirring, reaction is carried out until the epoxide equivalent of the epoxy resin ranges from 1300 to 2400; 3, the alcohol ether solvent is added, the temperature is reduced to 50 to 65 DEG C, phosphoric acid is added, the temperature is increased to 90 to 135 DEG C so as to obtain an epoxy phosphate; and 4, cooling is carried out,an amine neutralizer is added, uniform stirring is carried out, deionized water is added slowly, and emulsification is carried out. The properties, especially heat resistance, corrosion resistance, and insulation performance, of the obtained aqueous baking varnish are capable of reaching the level of the same kind solvent type epoxy baking varnish, and VOC emission amount is reduced at the same time, and environment protection performance is improved.