Environmentally friendly waterborne polyurethanes (WPUs) modified by moisture‐curable alkoxysilane have been much studied nowadays. In this work, a new diol‐bearing pendant urea‐propyl trimethoxysilane (APD‐Si) was synthesized and used as the chain extender in the preparation of a silicone‐modified WPU dispersion. Both the formation of hybrid networks based on the condensation of trimethoxysilane groups and the enhanced microphase separation of the hard and soft segments have been found to rely on the strong hydrogen‐bonding capability of the urea‐containing spacers, which link the alkoxysilane groups with the backbone of WPU. Because of the synergism of chemically bonded silsesquioxane and physically hydrogen bonded hard domains serving as crosslinking points, the mechanical properties of the hybrid films of WPU are improved, especially the modulus and yield strength. © 2018 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2018, 135, 46628.