The invention belongs to the technical field of hydrophobic coating materials and particularly relates to a fluorine-containing super-hydrophobic self-cleaning anti-fouling coating and a preparation method and application thereof.According to the method, silane monomer free radicals are polymerized to generate a polysiloxane polymer A with hydroxyl groups at the tail end; then hydroxyl-terminated perfluoropolyether and isocyanate react to prepare perfluoropolyether B with isocyanato; A and B react to prepare a fluorine-containing super-hydrophobic self-cleaning anti-fouling polymer, and the structure of silane monomers and the structure of hydroxyl-terminated perfluoropolyether are as shown in the formula I and formula II respectively; the polymer is cross-linked with a base body to obtain the super-hydrophobic self-cleaning anti-fouling coating.The coating has the super-hydrophobic property and can bring away most dust and dirt on the surface of a base material during rolling.Perfluoropolyether with low surface energy and a siloxane polymer capable of being attached to the base material firmly can be connected through isocyanato, the requirement for glass product self-cleaning in daily life of people can be met, and the preparation method is simple and suitable for industrial production.The formula I and the formula II are as shown in the description.