Fluorinated emulsifier-free polyacrylate emulsion with a core-shell structure was synthesized via the pre-emulsified seed emulsion polymerization, with methyl methacrylate (MMA), butyl acrylate (BA) and hexafluorobutyl methacrylate (HFMA) as the main monomers, and with ammonium allyloxtmethylate nonylphenol ethoxylates sulfate (DNS-86) as the polymerizable emulsifier. Then, the influences of the dosages of DNS-86 and HFMA on the electrolyte stability of the emulsifier-free emulsion and on the water resistance of the film were discussed. Moreover, the emulsion and the film were characterized by means of FT-IR, TEM, DSC, contact angle method and TG. The results show that, as compared with the traditional complex emulsifier OP-10/SDS, polymerizable emulsifier DNS-86 may result in stronger electrolyte stability and water resistance in the polymerization with 2.2% DNS-86 and 8% HFMA, that HFMA effectively participates the emulsion copolymerization, that there exists a clear core-shell structure in emulsion particles, that the emulsifier-free emulsion film is of two glass transition temperatures, namely 261.11 and 300.48 K, which respectively correspond to the core-phase and the shell-phase copolymers, and that, at a HFMA dosage of 8%, the water contact angle of the film-air interface reaches 94.1 and the decomposition temperature of the emulsifier-free emulsion film is 48 K higher than that of the traditional polyacrylate emulsion film, showing a greatly-improved hydrophobic property and thermal stability of the film.