Soy-based adhesives have garnered significant attention owing to their distinctive environmentally sustainable characteristics and low cost. However, they exhibit inadequate bonding strength and water-resistance, which can be attributed to the presence of polar groups in soy flours. Herein, a simple and eco-friendly dual-crosslinking strategy was proposed to manufacture a soy-based adhesive (SF/IO4/CA adhesive) with excellent mechanical properties and good water-resistance. Specifically, soy flours were treated with sodium periodate (NaIO4) for oxidization, which facilitated the soy flours' self-crosslinking process by converting carbohydrates into components having the cross-linking action (internal cross-linking agents). Then, incorporating the citric acid (CA) would promote to the carboxyl groups (-COOH) of CA to react with the hydrophilic hydroxyl groups (-OH) present in soy flours by esterification reaction. The findings demonstrated that a high-performance plywood using SF/IO4/CA adhesive was successfully produced, which shear strength of cold-water (20 °C for 24 h), hot-water (63 °C for 3 h), and boiling-water (93 °C for 3 h) reached 1.69 MPa, 1.68 MPa, 1.72 MPa, and 1.47 MPa, respectively. The soy-based adhesive has excellent mechanical strength and water-resistance due to its dual-crosslinking network system, which has significant promise for application use in the wood-based panels industry.