Three kinds of cellulose nanocrystals (CNCs) were added into waterborne polyurethane (WPU), and nanocomposite films were prepared by solution casting method. The influence of different ionic function groups on microstructure and properties of composite films was investigated, and interaction mechanism between these two components was analyzed. Results show that thermal stability of these composite films are improved by 15℃. Compared with sulfated CNCs (SCNCs) and TEMPO oxidized CNCs (TOCNCs), FE-SEM results prove that cationized CNCs (CaCNCs) have better dispersion in composite films. In addition, fracture surface did not display large cavities, which indicates the interface binding force between WPU and CaCNCs is stronger. The tensile strength and fracture work of CaCNC/WPU composite film increase by 11.9% and by 8.4%, respectively. The oxygen permeability of CaCNC/WPU composite film is the lowest in these composite films, which is 5.00 cm3•cm (cm2•s•Pa)-1. Water vapor permeability of composite films may have a close positive correlation with their hygroscopicity. In all, composite film with CaCNCs has optimal strength, toughness, light transmittance and oxygen barrier properties. There may be opposite ion attraction superimposed hydrogen bond between CaCNCs and WPU in the composite film. The composite films are expected to have applications in food packaging, furniture coatings and biomedical applications.