The invention discloses fluorine-containing bi-functional microspheres and application thereof. The fluorine-containing bi-functional microspheres have a structure shown as a formula (I), wherein B is crosslinked polymer microspheres, silicon dioxide microspheres, aluminum oxide microparticles or ferroferric oxide microparticles; g represents grafting; FL is a structural unit containing fluorine element; G is a structural unit containing hydroxyl, amido, carboxyl or an epoxy group; A is a structural unit containing hydroxyl, amido, carboxyl or an epoxy group; E1 and E2 are hydrogen, halogen or sulfydryl; x is 0 or 1; y is 0 or 1; and m is a natural number more than or equal to 0, and n is a natural number more than or equal to 0. The fluorine-containing bi-functional microspheres can be used for modifying surfaces of materials to form a hydrophobic and oleophobic coating. In the process of fluorination modification of the microspheres, a certain amount of hydroxyl and carboxyl are retained, and the microspheres are fixed on the surfaces of the materials under the action of a covalent bond of the retained hydroxyl and carboxyl and an adhesive, so that the stability of the coating is improved and the coating is not easy to fall off and deform.