Traditional two-component waterborne polyurethane (2K WPU) has low water resistance, which limits its application in the wide field. In this work, fluorine-modified 2K WPU films (2K-WFPUs) were successfully prepared using a fluorine-modified acrylate emulsion as hydroxyl component and a hydrophilically modified polyisocyanate as curing agent. Fourier transform infrared spectroscopy, scanning electron microscopy, and X-ray photoelectron spectroscopy analysis indicate that hexafluorobutyl acrylate (HFBA) was successfully introduced into the 2K-WFPUs. The effects of HFBA content on the surface, thermal stability, water resistance, mechanical, and application properties of 2K-WFPUs were investigated. Compared with the unmodified film, with the increase in HFBA level from 0 to 8%, the static water contact angle of 2K-WFPUs increased from 66 degrees to 92 degrees, the surface-free energy decreased from 42.7 to 28.4 mJ m-2, the water absorption reduced from 15.9 to 9.9%. Thermogravimetric analysis shows that the thermal stabilities of 2K-WFPUs were improved remarkably. Meanwhile, adding HFBA did not weaken the impact resistance, flexibility, and adhesion of 2K-WFPUs and maintained the highest level. The fluorine-modified 2K WPU coatings have potential application in wood furniture and automotive finishing.