The invention relates to a bio-based super-hydrophobic coating and a preparation method and an application method thereof, the bio-based super-hydrophobic coating comprises a primer and a top coating,and the top coating is prepared from resin B, lotus leaf particles, a pigment, a thickener, an acid-base regulator and the like. According to the bio-based super-hydrophobic coating as well as the preparation method and the application method thereof, the resin B is used as a matrix, the lotus leaf particles belonging to pure organisms are crushed and ground through a specific process, a nano-micron dual structure of lotus leaves is reserved, and the lotus leaf particles are added into an environment-friendly coating matched with the the lotus leaf particles. The primer is firstly coated or sprayed on a surface to be hydrophobic to ensure adhesion, reduction of surface energy and adhesion of the coating due to addition of e thlotus leaf particles is avoided, then the top coating is coatedor sprayed on the surface to be hydrophobic, the water contact angle after coating is larger than 150 degrees, the synthesis process is simple, the cost is low, and the coating is green, environmentally friendly, safe and pollution-free and can be produced in batches. The super-hydrophobic self-cleaning coating can be widely applied to the surfaces of wall surfaces, cement, metal, glass and the like to realize super-hydrophobicity and self-cleaning.