Chemical modification of soy protein, via crosslinking, is the preferred method for creating non-toxic, renewable, environmentally friendly wood adhesives. The denaturing process of protein is important for the adhesive performance improvement. In order to investigate the effect of different denaturing agents on the performance of soy protein-based adhesives before and after crosslinking modification. In this study, three different denaturing agents—urea (U), sodium dodecyl sulfate (SDS), and sodium hydrogen sulfite (SHS) and an epoxide crosslinking agent—Triglycidylamine (CA) were used to prepare soy protein-based adhesives. The results showed: (1) The denaturing agent unfolded protein molecules and exposed more hydrophobic groups to prevent water intrusion, which was mainly a contribution for the water resistance and performance improvement of soy protein-based adhesives. The wet shear strength was improved up to 91.3% (denaturing by urea). (2) After modifying by the crosslinking agent, the properties and performance improvement was due to the fact that the active groups on soybean protein molecules reacted with the crosslinking agent to form a crosslinking structure, and there is no obvious correlation with the hydrophobic groups of the protein. (3) The unfolded soybean protein molecules also expose hydrophilic groups, which facilitates the reaction between the crosslinking agent and protein to form a denser crosslinking structure to improve the performance of the adhesive. Particularly, after denaturing with SHS, the wet shear strength of the plywood bonded by the SPI-SHS-CA adhesive increased by 217.24%.