Different structures of siloxanes possess different properties. Therefore, diphenylsiliconediol (DPSD) and polydimethylsiloxane (PDMS and KF-2201) were selected to modify the representative anionic waterborne polyurethane through chemical bonding. The different structures of siloxanes which could optimized the structures of waterborne polyurethane were bonded to the macromolecular chains for improving water resistance and heat resistance, and the corresponding emulsion and films were prepared. By testing the water contact angle, water absorption, thermal weight loss, surface/fracture cross-sectional morphology, and other indicators of the waterborne polyurethane films, the differences in water resistance and heat resistance of the three modified films were explored. The research results showed that the surface, normal fracture cross-section, and liquid nitrogen brittle fracture cross-section of the modified films were smoother, and there was significant phase separation of soft and hard segments. XPS analysis showed that the Si-O segments of the films were easy to migrate to the surface, while the microphase separation of the soft and hard segments and the migration of the Si-O segments of the films could improve the water resistance and heat resistance of the films. Therefore, KF-2201 containing Si-O bond and hydrophobic benzene ring was more helpful to improve the water resistance and heat resistance of the films. The water absorption rates of the unmodified films, DPSD, PDMS, and KF-2201 modified films were 16.41%, 12.7%, 10.19%, 9.12%, and the water contact angles were 81.08?, 96.37?, 105.72?, 110.05?, when the thermal weight loss was 95%, the temperature was 367℃, 375℃, 394℃, 401℃.