Fluoropolymers play an essential role in electrowetting (EW) systems. However, no fluoropolymer possesses the desirable properties of both hydrophobicity and dielectric strength. In this study, for the first time, we report the integration of two representative fluoropolymers-namely, Teflon AF (AF 1600X) and Cytop (Cytop 809A)-into one bifunctionalized dielectric nanolayer. Within this nanolayer, both the superior hydrophobicity of Teflon AF and the excellent dielectric strength of Cytop were able to be retained. Each composed of a 0.5 μm Cytop bottom layer and a 0.06 μm Teflon AF top layer, the fabricated composite nanolayers showed a high withstand voltage of ~70 V (a dielectric strength of 125 V/μm) and a high water contact angle of ~120°. The electrowetting and dielectric properties of various film thicknesses were also systemically investigated. Through detailed study, it was observed that the thicker Teflon AF top layers produced no obvious enhancement of the Cytop/Teflon AF stack.