Utilizing corn starch as a main raw material to prepare starch adhesive, polyvinyl alcohol, borax, and carboxymethyl cellulose (CMC) were added in the preparation process. Because of the poor water resistance of native starch adhesive, an isocyanate prepolymer as a cross-linking agent was synthesized and added to improve its water resistance. Three-layer wood panels were fabricated and bonding strength was measured. The differential scanning calorimeter (DSC), thermogravimetric analysis (TGA), scanning electron microscopy (SEM), X-ray photoelectron spectroscopy (XPS), and energy dispersive X-ray spectroscopy (EDX) were used to characterize the thermal properties, morphology, and element content of samples. Effects of R value (the molar ratio of isocyanate group to hydroxyl group) and CMC addition on the physicochemical properties of starch adhesive were investigated. Thermal analysis results showed prepolymer/starch adhesive (PSA) cured at a relatively low temperature and thermal stability was improved after prepolymer added. SEM, XPS, and EDX results revealed that prepolymer played an effective role in bonding process, and the penetration of adhesive occurred in the wood, resulting in the improvement of bonding strength.