The invention relates to the technical field of paint processing and particularly relates to waterproof polyurethane paint and a preparation method thereof. The waterproof polyurethane paint comprises, by weight, 30 to 50 parts of dimethyl ether, 20 to 30 parts of polyvinylidene chloride, 35 to 50 parts of a long-chain polyether, 35 to 50 parts of isocyanate, 40 to 50 parts of polyether polyol, 10to 30 parts of light calcium carbonate powder, 10 to 15 parts of glass fiber powder, 12 to 18 parts of perlite powder, 5 to 10 parts of mica powder, 5 to 10 parts of an inorganic flame retardant, 1 to 3 parts of a film forming aid, 0.2 to 0.5 parts of a dispersant, 5 to 10 parts of a bactericide, 0.3 to 1.5 parts of a leveling agent and 4 to 6 parts of deionized water. The long-chain polyether isused for surface modification and then is mixed with other components. The waterproof polyurethane paint has low thermal conductivity, a high closed cell ratio, good waterproofing effects and good environmental friendliness.