Waterborne fluorinated polyurethane-acrylate hybrid emulsion modified by long aliphatic chains (WFPUA) is prepared by two steps, which include that the stearyl alcohol (SA)-blocked (end-capped) polyurethanes (SPU) are carried out in the mixtures of vinyl monomers, and then, the WFPUA is prepared via the free radical polymerization after the pre-emulsification of the said system. The characteristic of the reaction is the phase-inversion polymerization. The results show that the emulsifiability of SPU is firstly improved then decreased with the continuous increase in SA content. When the molar ratio of SA to 2-hydroxyethyl methacrylate (HEA) in the SPU is 1:1, the stability, zeta potential, viscosity and particle sizes of the WFPUA emulsion have the best results. The mechanical properties of WFPUA hybrid films deteriorate with the increase in SA content at 20 degrees C, but the mechanical properties of WFPUA films with more SA content achieve better results at 80 degrees C. The fluorinated groups migrated to the surfaces more easily with more SA content. In order to form the liquid crystalline-like structure on the WFPUA's surface, the gradient heating treatment to an elevated temperature (i.e., 120 degrees C) to properly orient the fluorinated chains is necessary.