The invention provides a waterproof polyurea coating and a preparation method thereof. The waterproof polyurea coating comprises a component A and a component B, wherein the component A comprises 3,3-dimethyl- 4,4-diisocyanatodicyclohexylmethane, polyether glycol and a solvent; and the component B comprises aminopolyether, an amine chain extender, a plasticizer and silane-modified nanometer lithopone. According to the waterproof polyurea coating, 3,3-dimethyl-4,4-diisocyanatodicyclohexylmethane is used as the raw material, so that the light stability and weather resistance of the waterproof polyurea coating are improved, the problem that a coating prepared by taking an aromatic compound as a raw material is easily aged is solved, the coating is kept to have long enough gelling time and curing time, and the coating is relatively good in permeation and combination with a substrate. The silane-modified nanometer lithopone is adopted, so that the corrosion resistance and ageing resistance of the coating are improved; and ultraviolet is effectively absorbed, and a photocatalytic reaction is carried out, so that the coating has antibacterial property, and the pollution resistibility of the coating is improved.