To construct waterborne polyurethane with excellent water resistance and mechanical properties, an organic‐inorganic hybrid nanocomposite based on modified halloysite nanotubes (mHNTs) and polyurethane was prepared. The HNTs were modified with an amino‐silane coupling agent (KH550) and then reacted with polypropylene glycol, 2,2‐Dimethylol propionic acid, and Toluene diisocyanate to form mHNTs/PU aqueous dispersions. The structure of the siloxane functionalized mHNTs was confirmed by a Fourier transform infrared study. The PU/mHNTs composites were characterized by using differential scanning calorimetry, scanning electronic microscopy, thermal gravimetric analysis, a tensile test, particle size analysis, and a water swelling experiment. The tensile strength, Young's modulus, and elongation at the break of the composite polymer with 0.5 wt % mHNTs was shown to be significantly improved, by approximately 200%, 200%, and 30%, respectively. An excess amount of mHNTs could weaken the reinforcing effect and stability of the composite emulsion. © 2016 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2016, 133, 43949.