Developing eco-friendly, high-performance adhesives is crucial for sustainable industrial applications but remains a significant challenge. Herein, a synergistic strategy combining core-shell hybridization and borate chemistry was employed to fabricate a multifunctional soy protein (SPI) adhesive with excellent adhesion. Specifically, a reactive core-shell hybrid (POSS-U) was synthesized via free-radical polymerization using octavinyl-POSS as the core and urushiol (U) as the shell. Sodium borate (SB) was then added as a crosslinker, along with POSS-U and SPI, to prepare the SPI/POSS-U/SB adhesive. The SPI/POSS-U/SB adhesive exhibited a 100% increase in dry shear strength (2.46 MPa) and a wet shear strength of 0.74 MPa, meeting indoor application standards. Due to the thermal shielding and char formation of POSS and SB, the peak heat release rate of the modified adhesive reduced by 25.4%, revealing excellent flame retardancy. Additionally, the modified adhesive remained mold-free for 144 h due to the antifungal properties of urushiol and boron. This work provides an innovative approach for enhancing protein-based adhesives and contributes to the advancement of multifunctional composite materials.