From an environmentally sustainable perspective, soybean meal (SM) adhesive presents an ideal alternative to petrochemical-based adhesives. Generally, strength and toughness are mutually exclusive for an adhesive. Hence, the creation of protein-based adhesives with high water-resistant strength of bonding, remarkable toughness, and multifunctionality remains a notable challenge. This study reports a dual hyperbranched siloxane nanocluster cross-linking strategy for creating SM-based adhesives with superior performance. In detail, synthesized hyperbranched epoxy siloxane nanocluster (ESN) and hyperbranched phenylboronic acid siloxane nanocluster (BPA@SN) were introduced into the SM matrix to establish a targeted crosslinking network between epoxy groups and protein chains as well as phenylboronic acid and polysaccharides. Meanwhile, the flexible Si−O segments within the hyperbranched siloxane facilitated energy dissipation, significantly boosting the adhesive toughness. After cross-linking modification, SM/ESN/BPA@SN-1 adhesive demonstrated outstanding dry bonding strength (2.04 ± 0.18 MPa), water-resistant bonding strength (1.12 ± 0.06 MPa), and toughness (18.5 ± 4.02 kJ/m 3 ). Moreover, the adhesive exhibited distinctly improved resistance to mold, thermal stability, and flame retardancy. Therefore, this new strategy of using functional hyperbranched siloxane nanoclusters and SM to design strong, tough, and multifunctional green and sustainable wood-based biomass adhesives provides new ideas for achieving green development.