Response surface methodology was employed to determine the effects of enzymatic pretreatment temperature, time, and pH on the reducing sugar content and bonding strength of soy-based adhesives (SBAs). Plywood specimens bonded by the SBAs with Pinus massoniana veneer were then produced. A significant positive correlation was observed between reducing sugar content and the bonding strength of SBAs. The effects of pretreatment temperature and time on bonding strength were also significant, but insignificant with respect to reducing sugar content; the effects of enzymatic pretreatment time on response values were the smallest. The optimal enzymatic pretreatment conditions of SBA were a pretreatment temperature of 54 °C, a pretreatment time of 20.0 min, and a pretreatment pH of 5.1. Under these conditions, the reducing sugar content and bonding strength (boiling-water test) of SBAs were 2.93% and 0.62 MPa, which were higher than the control by 113.9% and 30.6%, respectively. X-ray diffraction (XRD) indicated that the ordered degree of soy protein decreased, but the ordered structure had no variation when defatted soy flour was treated by enzymes with combination of acid, salt, and alkali. The SBAs contain more active functional groups and have better water resistance after curing.