The invention discloses an organic modified waterproof paint which comprises the following raw materials in part by weight: 30 to 35 parts of isocyanate, 25 to 30 parts of polyether, 15 to 20 parts of modifier, 20 to 25 parts of sodium methyl silicate, 5 to 8 parts of ferrum dioxide, 11 to 15 parts of silicon dioxide, 6 to 9 parts of sodium carbonate, 40 to 45 parts of deionized water, 13 to 16 parts of perlite, 12 to 15 parts of nano mica, 3 to 6 parts of chlorine dioxide, 4 to 7 parts of bentonite, 7 to 9 parts of polyacrylamide and 3 to 5 parts of polydimethylsiloxane. A preparation method of the organic modified waterproof paint comprises the following steps of: S1, adding the isocyanate, the polyether and the deionized water into a stirrer, and stirring for 2 to 3 hours at a temperature of 40 to 45 DEG C at a stirring speed of 35 to 45rpm; S2, adding the modifier, the sodium methyl silicate, the ferrum dioxide, the silicon dioxide and the sodium carbonate, and then stirring for 5 to 6 hours at a stirring speed of 20 to 25rpm. The organic modified waterproof paint has excellent waterproofness, high tensile strength and excellent flexibility, is simple in construction, healthy and environmental-friendly, and takes a very important effect on concrete construction.