The development of formaldehyde-free functional wood composite materials through the preparation of strong and multifunctional soybean protein adhesives to replace formaldehyde-based resins is an important research area. However, ensuring the bonding performance of soybean protein adhesive while simultaneously developing thermally conductive adhesive and its corresponding wood composites is challenging. Taking inspiration from the microphase separation structure of spider silk, boron nitride (BN) and soy protein isolate (SPI) were mixed by ball milling to obtain a BN@SPI matrix and combined with the self-synthesized hyperbranched reactive substrates as amorphous region reinforcer and cross-linker triglycidylamine to prepare strong and thermally conductive soybean protein adhesive with cross-linked microphase separation structure. These findings indicate that mechanical ball milling can be employed to strip BN followed by combination with SPI, resulting in a tight bonded interface connection. Subsequently, the adhesive's dry and wet shear strengths increased by 14.3% and 90.5% to 1.83 and 1.05 MPa, respectively. The resultant adhesive also possesses a good thermal conductivity (0.363 W/mK). Impressively, because hot-pressing helps the resultant adhesive to establish a thermal conduction pathway, the thermal conductivity of the resulting wood-based composite is 10 times higher than that of the SPI adhesive, which shows a thermal conductivity similar to that of ceramic tile and has excellent potential for developing biothermal conductivity materials, geothermal floors, and energy storage materials. Moreover, the adhesive possessed effective flame retardancy (limit oxygen index = 36.5%) and mildew resistance (>50 days). This bionic design represents an efficient technique for developing multifunctional biomass adhesives and composites.