Under the action of initiator(BPO), the α-methyl acrylic acid (α-MAA), butyl hexafluorobutyl methacrylate (HFMA) and other monomers are graft copolymerized into epoxy molecular. By adding N, N-dimethyl ethanolamine, fluorine-containing water-based epoxy resin emulsion can be prepared. By orthogonal experiments, the amount of acrylic monomer, BPO dosage, grafting temperature and other optimum conditions can be determined. Infrared spectroscopy (FT-IR) characterization confirms acrylic monomers successfully grafted to the epoxy resin molecules. The study focuses on the effect of different content of HFMA on modified emulsion particle size and contact angle of coating. The results shows that the introduction of HFMA monomer made the smallest average particle size of emulsion low to 165 nm, and the contact angle against water is increased by 20°. After determining the conventional and environmental performance of the emulsion, the results shows that this preparation of epoxy resin emulsion can fully meet the requirements of waterborne coatings.