Most wood-based panels were currently prepared using aldehyde-based adhesives, making the development of natural, renewable, and eco-friendly biomass-based adhesives a prominent area of research. Herein, the phenolic resin was modified using a soybean protein isolate (SPI) treated with a NaOH/urea solution through a copolymerization method. The physicochemical properties, chemical structure, bonding properties, and thermal properties of the soybean protein-modified phenolic resin (SPF-U) were analyzed using Fourier transform infrared spectroscopy, thermogravimetric analysis, and formaldehyde emission tests. The results indicated that the molecular structure of the soy protein isolate degraded after NaOH/urea solution treatment, while the gel time was gradually shortened with increasing NaOH/urea solution-treated soy protein isolate (SPI-U) dosages. Although the thermal stability of the soy protein isolate was lower than that of the phenolic resin, the 20% SPF-U resin demonstrated better thermal stability than other modified resins. The PF modified with 30% SPI-U (SPF-U-3) exhibited the lowest curing peak temperature of 139.69 °C than that of the control PF resin. In addition, all modified PF resins exhibited formaldehyde emissions ranging from 0.18 to 0.38 mg/L when the SPI-U dosage varied between 20% and 50%, thereby meeting the E0 plywood grade standard (≤0.5 mg/L).