Soy protein isolate (SPI) has attracted considerable attention in the field of packaging technology due to its easy processability, biodegradability, and good film-forming characteristics. However, SPI-based films often suffer from inferior mechanical properties and high moisture sensitivity, thus restricting their practical application. In the present study, herein, a biobased nanocomposite film was developed by cross-linking SPI matrix from the synergistic reinforcement of cellulose nanofibers (CNF) and nano-silica (NS) particles. First, we functionalized the CNF with NS using a silane agent (KH560) as an efficient platform to enhance the interfacial interaction between SPI and CNF/NS, resulting from the epoxy-dominated cross-linking reaction. The chemical structure, thermal stability, and morphology of the resultant nanocomposite films were comprehensively investigated via Fourier transform infrared (FTIR) spectroscopy, X-ray diffraction (XRD), scanning electron microscopy (SEM), and thermogravimetric analysis (TGA). These results supported successful surface modification and indicated that the surface-tailored CNF/NS nanohybrid possesses excellent adhesion with SPI matrix through covalent and hydrogen-bonding interactions. The integration of CNF/NS into SPI resulted in nanocomposite films with an improved tensile strength (6.65 MPa), representing a 90.54% increase compared with the pristine SPI film. Moreover, the resulting composites had a significantly decreased water vapor permeation and a higher water contact angle (91.75°) than that of the unmodified film. The proposed strategy of synergistic reinforcements in the biobased composites may be a promising and green approach to address the critical limitations of plant protein-based materials in practical applications.