Conventional waterborne polyurethane (WPU) has poor water resistance and poor overall performance, which limits its application in outdoor coatings. A solution to this problem is urgently needed. The introduction of fluorine-containing groups can effectively improve the water resistance of WPU. In this study, a new fluorinated chain extender (HFBMA-HPA) synthesized by free radical copolymerization and epoxy resin (E-44) were used to co-modify WPU, and five waterborne fluorinated polyurethane (WFPU) emulsions with different fluorine contents were prepared by the self-emulsification method. The effects of HFBMA-HPA content on the emulsion particle properties, coating surface properties, mechanical properties, water resistance, thermal stability, and corrosion resistance were investigated. The results showed that the WFPU coating had excellent thermal stability, corrosion resistance, and mechanical properties. As the content of HFBMA-HPA increased from 0 wt% to 14 wt%, the water resistance of the WFPU coating gradually increased, the water contact angle (WCA) increased from 73° to 98°, the water absorption decreased from 7.847% to 3.062%, and the surface energy decreased from 32.8 mN/m to 22.6 mN/m. The coatings also showed impressive performances in the adhesion and flexibility tests in extreme conditions. This study provides a waterborne fluorinated polyurethane material with excellent comprehensive performance that has potential application value in the field of outdoor waterproof and anticorrosion coatings.