Waterborne cationic fluorinated polyurethane (WCFPU) was prepared by the reaction of isophorone isocyanate (IPDI), polyether polyol (PTMG1000), N-methyldiethanolamine (MDEA), trimethylol propane (TMP) and 2-(perfluorooctyl) ethyl alcohol (FEOH) and then the films of the WCFPU were prepared. Their structure, surface property, mechanical properties, thermal performance and chemical resistance of their membrane were characterized by fourier transform infared spectrometer (FT-IR), interfacial tension instrument (IT), contact angle (CA), thermogravimetry (TG) and spot test. The results revealed that WCFPU was endowed with good mechanical properties and low surface energy of its film. TG diagrams also revealed that the application range of product was enlarged. It was also found that the fluorinated polyurethane had outstanding chemical resistance.