The invention discloses a waterborne fluorocarbon coating, and a preparation method and application thereof. A formula for raw materials of the waterborne fluorocarbon coating comprises 13.0 to 48.0% of a waterborne fluorocarbon emulsion, 1.0 to 3.0% of hydroxyethyl cellulose, 10.5 to 18.8% of an inorganic pigment, 18.2 to 32.2% of a filling material, 5.0 to 7.0 % of wear-resistant powder, 0.6 to 2.3% of a wetting dispersant, 0.5 to 1.0% of a multifunctional auxiliary agent, 0.1 to 0.5% of a de-foaming agent, 0.4 to 4.0% of a bactericide, 0.1 to 3.2% of a thickening agent, 0.6 to 3.0% of a film forming auxiliary agent, 1.0 to 4.2% of an anti-freezing agent and 14.0 to 20.0% of water, wherein the pH value of the waterborne fluorocarbon coating is 8.0 to 9.5, and the Moh's hardness of the wear-resistant powder is more than 9.0. The waterborne fluorocarbon coating has no toxicity, no pollution and both functions of decoration and protection; a paint film formed by the coating has good wear resistance and weatherability and can improve anti-corrosive performance and wear resistance of a regenerated woodwork.