In this study, biodegradable films were prepared from soy protein isolate (SPI), glycerol, and ethylene glycol diglycidyl ether (EGDE). To enhance the mechanical properties of the films, cellulose nanocrystal (CNC) was employed as reinforcement. CNC was also modified with a silane coupling agent (MCNC) for introducing superficial amino groups. As a result, the interaction between the MCNC and SPI matrix was enhanced by forming the chemical-crosslinking network through the reaction between amino and epoxy groups, thus enhancing physical properties. The mechanical properties, hydrophobic properties, water resistance, and thermal stabilities of the obtained films were then fully analyzed. Results showed that, in a comparison of the un-modified and CNC modified films, the mechanical properties and water resistance of the modified SPI films were improved considerably after the incorporation of MCNC. The tensile modulus and tensile strength of the CNC modified films increased by 128.3% and 53.0%, respectively, compared to the un-modified SPI films, resulted from the formation of hydrogen bonding and physical crosslinking structures between CNC and matrix. The tensile modulus and tensile strength of the MCNC modified films increased by 212.7% and 90.1%, respectively, due to the chemical-crosslinking network achieved among SPI, MCNC, and EGDE. It was also accounted for the improvement of the thermal stabilities and water resistance of the MCNC-modified SPI films.