Soybean lipophilic protein (SLP) is a highly hydrophobic protein rich in phospholipids, which is the key to solve the functional defects of soybean protein isolates, such as hydration properties and interfaces properties, etc. The dissociation-association behavior and self-assembly nanoparticles of SLP induced by heating were characterized by some modern technology means, which were the ultraviolet spectrum, fluorescence spectrum, circular dichroism spectrum, Fourier transform infrared, thermal analysis and gel electrophoresis techniques. The results showed that the heating treatment transition zone of SLP was 80~90℃, where the SLP can basically maintain a natural structure without significant changes when the heating treatment temperature was below 80℃. While the secondary conformation of SLP was changed significantly when the heating treatment temperature was above 90℃. The molecular structure of the SLP was dissolved and extended to maximum extent, with increased surface hydrophobicity at 90℃ for 20min. Subsequently, the SLP self-assembled to form a stable single-distributed nanoparticle system with a particle size of about 110nm. The dissociate subunits were reassembled into intermediate aggregates by interaction of disulfides and hydrophobic interaction, resulting in an increase of the degree of intermolecular aggregation and structural stability. The research result would provide theoretical support for the development of SLP-specific powder and its application in the food field.