The invention discloses a waterproof environment-friendly anti-corrosive coating and a preparation method thereof. The waterproof environment-friendly anti-corrosive coating contains the following raw materials in parts by weight: 20-50 parts of bisphenol A epoxy resin, 2.1-4.6 parts of 1-alkylindole-3-acetic acid, 0.4-1.1 parts of casein glue, 0.2-1.3 parts of phenyl carbamate, 2.5-3.4 parts of nano titania, 10-12 parts of diatomite, 3-5.7 parts of tetrachlorophthalic acid anhydrite, 2.7-3.5 parts of talc powder, 1.8-2.9 parts of nano tungsten carbide powder, 3.5-5.1 parts of alkyl amidopropyl dimethylamine, 1.3-3.6 parts of polydimethyl siloxane, 0.8-2.2 parts of disodium dihydrogen pyrophosphate, 0.6-2.2 parts of methyl dihydrojasmonate, 2.3-4.8 parts of chromic anhydride, and 7.3-15 parts of calcium phosphate. The waterproof environment-friendly anti-corrosive coating disclosed by the invention has the advantages of high adhesion, high anti-corrosive performance, high hardness, strong chemical resistance, high water resistance, and strong salt spray resistance, as well as simple preparation method, long service life, good safety, environment friendliness, low production cost, and good economic efficiency.