In order to prepare waterborne polyurethane with excellent water resistance and thermodynamic properties, a series of side chain fluorinated waterborne polyurethane‐urea (FWPU‐UA) was synthesized with polytetramethylene ether glycol, N‐(2‐methyl‐1,3‐propanediol‐2′‐)‐perfluoro‐1‐butanesulfonyl amine (NPBA), isophorone diisocyanate, and isophoronediamine. With the increase of NPBA content, the weight loss temperature, glass transition temperature, and tensile strength of FWPU‐UA were all improved. Gaussian fitting analysis of infrared data and density functional theory simulation proved that the introduction of fluorine side chains increased the interaction of hydrogen bonding in the FWPU‐UA. X‐ray photoelectron spectroscopy analysis indicated that the aggregation of fluorine atoms on the surface of film were caused by the migration and enrichment of fluorine side chains. Furthermore, the water resistance of polyurethane‐urea film could be significantly improved by adding a small amount of NPBA, and the seven‐day water absorption rate of polyurethane‐urea film was reduced from 30.13% to 12.55%.