The present invention provides a waterborne self-polishing antifouling paint and a preparation method and application thereof, and belongs to the technical field of marine antifouling paints. The waterborne self-polishing antifouling paint provided by the present invention includes the following components in parts by weight: 30-60 parts of waterborne self-polishing emulsion, 30-70 parts of waterborne slurry, 0.1-0.5 parts of waterborne leveling agent, 0.2-1 parts of waterborne defoamer, 0.5-1 parts of film-forming additive and 10-20 parts of water. The waterborne self-polishing antifouling paint provided by the present invention has an ultra-low content of volatile organic compounds (VOCs) (less than 20 g/L), and is environmentally friendly. The waterborne self-polishing antifouling paint can be formed into a paint film with good mechanical properties, stable self-polishing rate, and excellent water immersion resistance and antifouling performance.