The invention relates to a waterproof coating, in particular to a high molecular waterproof coating and a preparation method thereof. The high molecular waterproof coating is prepared from a powder material and a liquid material in the weight ratio of (1-5):1, wherein the powder material comprises the following components in parts by weight: 0.1-5 parts of reactive polysiloxane compound, 1-5 parts of polypropylene chopped fiber, 10-50 parts of quartz powder, 30-70 parts of calcium carbonate and 1-15 parts of bentonite; and the liquid material comprises the following components in parts by weight: 30-80 parts of polyvinyl acetate emulsion, 0.5-5 parts of thickening agent, 0.5-5 parts of sterilizing agent, 0.1-3 parts of organic silicon antifoaming agent and 10-40 parts of water. The high molecular waterproof coating has the advantages of no pollution to human bodies and the environment, readily-available raw materials, low cost, easiness for preparing, convenience for construction, safety, environment friendliness, excellent physical property, strong bonding force, high extensibility, prevention of water and rust and the like, and can be applied to waterproofness of indoor and outdoor buildings.