The invention discloses a two-component waterborne polyurethane colored paint and the preparation method. The components of the paint are 5 to 15 water, 0.2 to 0.5 dispersant, 0.1 to 0.3 antifoamer, 0.1 to 0.3 wetting agent, 3 to 25 paints, 0 to 50 fillers, 10 to 80 film forming resins, 0 to 5 film forming additives, 0.1 to 0.3 disinfectant, 0.1 to 0.3 antiflash rust agent, 0.5 to 2 thickeners, 1 to 20 hydrophilically-modified polyisocyanate. The preparation method is that water, dispersant, antifoamer, wetting agent, paints and fillers are dispersed evenly by a sand mill, a ball mill or a high-speed stirrer after stirring, and are added with film forming resins, film forming additives, disinfectant, antiflash rust agent and thickeners to gain the product-component A. The hydrophilically-modified polyisocyanate is component B. The component A and component B are mixed uniformly when using. The invention is characterized in that the invention does not adopt organic solvents, does not contain toxic paints and has no harm on the human body and environment, and the properties can reach the solvent two-component polyurethane paint, which can be produced to the primer, intermediate coat and finishing coat, and can be applied in the surface of the wooden ware, cement and metals.