The invention discloses a transparent waterborne waterproof coating for a building and a preparation method thereof. The transparent waterborne waterproof coating comprises the following components in percentage by mass: 70-80% of water soluble high polymer material, 0.8-1.6% of coalescing agent, 0.8-1.6% of accelerant, 0.5-1.0% of nano material, 0.02-0.06% of penetrating agent, 0.3-0.8% of ultraviolet absorbent, 0.5-1.2% of thickening agent, 0.1-0.3% of defoaming agent and the balance of water. The coating disclosed by the invention is pollution resistant, good in weather fastness, excellent in physical and mechanical properties, acid and alkali resistance and waterproof performance, and good in transparency, and the coating does not cover the bottom, so that the coating can maintain the appearance and feature of the building when in use; and meanwhile, the coating is simple to prepare, environment-friendly, free of pollution and convenient to use and can be both spray coated and crush coated, so that the coating can be widely applied to water resistance of building periphery or exterior wall so as to provide long-term waterproof protection for the building.