The development of bio-based adhesives comprised of low-cost, renewable, and accessible biomass resources with high adhesion and toughness is needed in wood-based panel industry. Herein, a novel cationic waterborne polyurethane (CWPU) emulsion was prepared with a hydrophobic long alkyl chain and catechol structure via thiol-ene click reaction and direct emulsification. Then, the obtained emulsions were applied as efficient crosslinkers to enhance the bonding performance of soybean meal (SM) adhesives. The catechol group on polyurethane acted as a secondary reaction platform that formed multiple hydrogen bonds with protein molecules to optimize the mechanical strength and adhesion toughness of the SM resins. In addition, the hydrophobic alkyl chains grafted intertwine and served as a “water-proofer” that hindered the intrusion of water molecules. Consequently, the modified SM/HD@CCWPU resin presented an impressive improvement in its wet bonding strength and toughness to 165.9% and 378.1%, respectively, compared with the pure SM resin. This efficient, ecofriendly, and low-cost design enables the utilization of agricultural byproducts instead of traditional formaldehyde-based products to prepare high-performance adhesives.