The invention relates to environment-friendly waterproof coating and a preparation method thereof. The coating comprises two parts: a component A, namely a superhydrophobic material, and a component B, namely a coating composition, wherein the component A, namely the superhydrophobic material, is prepared from the following components in parts by mass: 15 to 25 parts of graphene, 2.5 to 6 parts of a water-soluble cationic surfactant, 55 to 75 parts of a sodium silicate solution, 10 to 15 parts of 10% NaOH, 25 to 45 parts of a silanizing reagent and 8 to 15 parts of deionized water; the superhydrophobic material is obtained by performing silanizing treatment on the surface of the graphene by an electrochemical lamination method; the component B, namely coating composition, is prepared from the following components in parts by mass: 20 to 30 parts of lignin, 20 to 30 parts of starch, 16 to 18 parts of diatom ooze, 10 to 12 parts of ash calcium, 11 to 15 parts of ground calcium carbonate, 0.5 to 1 part of a defoaming agent, 0.8 to 1 part of a dispersing agent and 15 to 30 parts of deionized water; and the waterproof coating is prepared by mixing the component A, namely the superhydrophobic material, and the component B, namely coating composition. According to the environment-friendly waterproof coating and the preparation method thereof which are provided by the invention, environment-friendly biomass materials, such as the starch, the lignin, the diatom ooze and the like, are adopted, and the added superhydrophobic material makes up the defect that the diatom ooze and calcium powder absorb moisture easily, so uniform and excellent water resistance of the coating layer is achieved.