To enhance the mechanical and water-resistant properties of soy protein isolate (SPI) based films, hydrophobic TriSilanolPhenyl polyhedral oligomeric silsesquioxanes (POSS) was incorporated to modify the SPI films. POSS has three SiOH groups in a molecular, which is employed to cross-link SPI with the help of 3-Glycidoxypropyltrimethoxysilane (GPTMS). POSS is a structure of eight phenol groups, playing a critical role in improving the physical and mechanical properties. The X-ray diffraction (XRD) and attenuated total reflectance (ATR) Fourier transform infrared spectroscopy (FT-IR) were used to characterize the films. The degree of reaction of SiOH groups in the POSS was estimated to be 53.0% according with the absorbance of ATR FT-IR spectra. Although the elongation at break was reduced by 52.6%, the tensile modulus, tensile strength and 10% offset yield strength were significantly increased by 86.6%, 34.0% and 56.8%, respectively, due to the cross-linking reactions among SPI, GPTMS and POSS. The results of water-resistant tests showed that the 24-hour water absorption was dramatically reduced by 54.7%.