High-performance, water-resistant soy protein isolate-based adhesives have broad applications in the plywood manufacturing industry. However, they tend to be difficult to industrialize due to many hydrophilic groups in the molecular chain of soy protein. This paper proposes a facile, economic, and environmentally friendly method to introduce bio-based materials into soy protein isolate to build a high-performance, water-resistant network structure. By introducing the ultrasonicated pectin and carboxylated cellulose nanofiber into the soy protein isolate, the modified soy protein isolate-based hybrid adhesive exhibits excellent adhesive properties and water resistance. In the optimized condition, the wet shear strength increases from 0.63 MPa of the blank sample to 1.15 MPa, and the moisture absorption rate decreases from 22.22% to 14.00%. Furthermore, the toughness of the composite adhesive has been improved. The transition from hydrophilic to hydrophobic is due to the covalent cross-linking and multiple hydrogen bonds within the hybrid adhesive. This facile method offers a new way to replace harmful formaldehyde adhesives.