Waterproof agent of emulsion containing fluorine and silicone（FSE） was prepared by the method of gradient emulsion polymerization. The techniques of Fourier transform infrared spectroscopy, integral rotation contact angle and X ray photoelectron spectroscopy were used to analyze FSE latex film structure and its performance. The FSE waterproof agent was added into gypsum, and its effects and action mechanisms on flexural strength, compressive strength and water resistance of gypsum samples were studied. The research indicates that the fluorine and silicone monomers have been effectively introduced into the molecular structure of emulsion in the process of synthesis, which results in the latex film excellent hydrophobic performance. The FSE waterproof agent binds the crystal closely and reduces the porosity in the crystal to change the gypsum crystal morphology and improve the flexural strength and compressive strength of gypsum sample. The FSE latex film fills the microscopic pores and changes the inner surface energy of macropores of hardened gypsum, so the water resistance of gypsum sample is improved.