The present invention relates to a fluorine-containing polyether grafting modified waterborne polyurethane, the preparation and the application thereof, a structural general formula of polyurethane is as the formula, wherein, R1 is equal to a polyurethane soft-segment polyol structure, R2 is equal to a polyurethane hard-segment isocyanate structure, R3 is equal to a polyurethane hard-segment chain extender structure, R4 is equal to the fluorine-containing polyether; X is equal to NH and O; the preparation is that: the polyol and the isocyanate react to compound the polyurethane prepolymer, then the waterborne polyurethane are obtained through the chain propagation of a chain extender, then the waterborne polyurethane and the fluorine-containing polyether are carried out a grafting reaction in the big molecules, so as to synthesize the fluorine-containing polyether grafting modified waterborne polyurethane; the application is that: the present invention can be applied to aerospace, aviation, automobiles, electronics, textiles, carpets, leathers, paper making, packaging, washing, machinery, construction and other fields. The present invention adopts the water as the solvent and has no formaldehyde, no or low VOC emission, no bioaccumulation and no toxicity, which is a multifunctional, green, environment protective, water-proof and dirt-proof coating layer and fabric finishing agent.