The waterborne perfluoroacylic polyurethane composite (WFPUC) series were prepared by the emulsion polymerization (WFPUC-E) and the physical blending (WFPUC-B). WFPUC-E was prepared by polymerizing perfluoroalkyl ethyl acrylate (FA) and waterborne polyurethane (WPU), and WFPUC-B was prepared by blending FA copolymer and WPU. The structures of the synthesized WFPUC were identified by using FT-IR-ATR. The surface and thermal properties of the synthesized WFPUC were investigated by measuring contact angle, surface energy, and TGA. The surface energy of WFPUC-E was lower than that of WFPUC-B. The thermal stability of the WFPUC-B showed better than that of the WFPUC-E.