The invention discloses a fluorine-containing self-cleaning polymer and application thereof in a hydrophobic antifouling coating. The method for preparing the fluorine-containing self-cleaning polymer comprises the following steps: adding epoxy group-containing acrylic ester, siloxane group-containing acrylic ester and hydroxyl-containing acrylic ester into a solvent, adding an initiator, and introducing nitrogen to react; stopping the reaction after the system becomes sticky to prepare polymer containing epoxy group, siloxane group and hydroxyl; and adding the prepared reaction product, perfluoropolyether acyl fluoride and an acid-binding agent into the solvent, and reacting for 12-24 hours to prepare the fluorine-containing self-cleaning polymer. In the polymer preparing process, the reaction is each step has a relatively high yield, a simple method for reacting free radical polymer and groups is adopted, the process is simple, and the abrasion resistance is improved by introducing the epoxy group; and the hydrophobic antifouling coating is convenient to stored by adopting a stable siloxane group.