The invention discloses a self-repairing organic fluorine silicon modified polyurethane waterproof coating and a preparation method thereof, comprising the following raw materials in parts by mass: 60-80 parts of polytetramethylene ether glycol, 15-30 parts of perfluoropolyether glycol, iso 40-60 parts of phorone diisocyanate, 20-35 parts of 4,4'-dithiodiphenylamine, 20-30 parts of fluorine-containing hydroxyl silicone oil, 30-40 parts of tetrahydrofuran, 0.8-2 parts of dibutyltin dilaurate, 2-3 parts of Tween 80, 15-20 parts of nano-calcium carbonate, 5-10 parts of nano-hydroxycalcium phosphate, 10-20 parts of deionized water; the preparation method is as follows: S1: prepare polyurethane prepolymer; S2: mix 4 , 4'-dithiodiphenylamine and fluorine-containing hydroxyl silicone oil were dissolved in tetrahydrofuran, then polyurethane prepolymer was added, and stirred and reacted at 60°C for 3-6 hours under a nitrogen atmosphere; S3: Preparation of organic fluorine-silicon modified polyurethane waterproof coating . The present invention combines disulfide bond, shape memory effect, and organic fluorine silicon modification, and by introducing S-S, C-F, Si-O bonds into the polyurethane molecular chain, it significantly improves its hydrophobicity, oil repellency, high and low temperature resistance, Weather resistance, corrosion resistance and other properties.