A fluorine-containing polyacrylate copolymer emulsion was synthesized by a seed emulsion polymerization method, in which methyl methacrylate (MMA) and butyl acrylate (BA) were used as main monomers and hexafluorobutyl methacrylate (HFMA) as fluorine-containing monomer. The structure and properties were characterized by Fourier transform infrared spectrum (FT-IR), transmission electron microscopy (TEM), particle size analysis, X-ray photoelectron spectroscopy (XPS), contact angle (CA), differential scanning calorimetry (DSC) and thermogravimetry (TG) analysis. The FTIR and TEM result, showed that HFMA was effectively involved in the emulsion copolymerization, and the formed emulsion particles had a core-shell structure and a narrow particle size distribution. XPS and CA analysis revealed that a gradient concentration of fluorine existed in the depth profile of fluorine-containing emulsion film which was richer in fluorine and more hydrophobic in one side. DSC and TG analysis also showed that a clear core-shell structure existed in the fluorine-containing emulsion particles. and their film showed higher thermal stability than that of fluorine-free emulsion.