The core-shell polyacrylate latex particles containing fluorine and silicon in the shell were successfully synthesized by a seed emulsion polymerization, using methyl methacrylate (MMA) and butyl acrylate (BA) as main monomers, dodecafluoroheptyl methacrylate (DFMA), and c-(methacryloxy) propyltrimethoxy silane (KH-570) as functional monomers. The influence of the amount of fluorine and silicon monomers on the emulsion polymerization process and the surface properties of the latex films were discussed, and the surface free energy of latex films were estimated using two different theoretical models. The emulsion and its films were characterized by particle size distribution (PSD) analysis, transmission electron microscopy (TEM), Fourier transform infrared spectrum (FTIR), nuclear magnetic resonance ( 1 H-NMR and 19 F-NMR) spectrometry, contact angle (CA) and X-ray photoelectron spectroscopy (XPS), differential scanning calorimetry (DSC), and thermogravimetry (TG) analysis. The results indicate that the average particle size of the latex particles is about 160 nm and the PSD is narrow, the synthesized latex particles exist with core-shell structure, and a gradient distribution of fluorine and silicon exist in the latex films. In addition, both the hydrophobicity and thermal stability of the latex films are greatly improved because of the enrichment of fluorine and silicon at the filmair interface, and the surface free energy is as low as 15.4 mN/m, which is comparable to that of polytetrafluoroethylene (PTFE).