A series of waterborne polyurethane (WPU) dispersions modified with different contents of 3-aminopropyltriethoxysilane (APTES) were synthesized based on poly(1,6-hexyl 1,2-ethylcarbonate) diol (PHEC) and isophorone diisocyanate (IPDI), and the films were obtained by casting the dispersions on Teflon molds. Effects of APTES content on the particle size and viscosity of the dispersions were studied. The structure and properties of the resulting films were investigated by Fourier transform infrared spectroscopy, wide angle X-ray diffraction measurement, dynamic mechanical analysis, thermogravimetric analysis and mechanical testing. The experimental results showed that the incorporation of APTES played an important role in the enhancement of the water and toluene resistance and mechanical properties of the SPU films. Young's moduli and ultimate tensile strengths were improved from 8.0 to 451MPa and 6.5–19MPa respectively as the APTES content increased from 1wt.% to 20wt.%. The ability of scratch resistance was enhanced, when the content of APTES increased to 20wt.%, the 3H pencil could not mar the surface. Moreover, the transmittance spectra indicated that the coatings showed high transparence.