A novel fluoropolymer of epoxy-terminated poly(2,2,3,4,4,4-hexafluorobutyl methacrylate) (E-PHFMA) was synthesized and incorporated into epoxy resin to prepare thermosets. Gel permeation chromatography and H-1 nuclear magnetic resonance data obtained verified the synthesis and measured the structure of the polymer. In order to demonstrate the effect of epoxy group on the properties of the thermosets, the corresponding fluoropolymer without epoxy group was prepared and the properties of thermosets modified by two kinds of fluoropolymers were comparatively studied. The contact angle measurements indicated that the thermosets modified with E-PHFMA had a little worse hydrophobicity but better surface stability. Scanning electron microscopy revealed the surface morphologies of the modified thermosets before or after surface stability experiment. The results of differential scanning calorimetry and thermogravimetric analysis showed that the thermosets modified with E-PHFMA had higher thermal stability.