The waterborne fluorinated polyurethane–acrylate hybrid emulsion (WFPUA) was prepared by two steps, including the preparation of the fluorinated alcohol blocked polyurethanes (FBPU) in the mixtures of vinyl monomers and fluorinated monomers and then the free radical polymerization after the pre-emulsification of the said system. The effects of hydrophilic monomer (MDEA) on the surfactivity and the emulsifiability of the FBPU were firstly reported. Then, the particle size (d), zeta potential (ζ), and viscosity (η) of the WFPUA hybrid emulsion were characterized, respectively. At the same time, the surface properties and the mechanical properties of the films were investigated. The results show that the increase of MDEA is good for the emulsifiability and the lower surface tension of the FBPU. This increase improves the stability, the ζ and η, yet decreases the d of the WFPUA emulsion. However, it has disadvantages to the hydrophobic performance of the WFPUA films. When the content of the MDEA in the WFPUA is increased from 4.67 to 14.89 %, the surface free energies are increased from 22.22 to 27.28 mJ m−2 and the attenuation rate of the contact angle–time curve is increased from 0.3051° to 0.6290°/min. Also, with the increase of MDEA, the tensile strength and the shore hardness of the film are increased, but its elongation at break is decreased. The storage moduli of the film are enhanced remarkably. Meanwhile, the glass transition temperature of the soft segment [Tg(s)] is reduced and that of the hard segment [Tg(h)] is raised.