Soybean protein isolate-anthocyanin complex system was used as the object of study. The interaction between soybean protein and anthocyanin was explored by fluorescence spectroscopy, UV-Vis spectroscopy, Fourier transform infrared spectroscopy and circular dichroism. The effect of anthocyanins on the structure of soybean protein isolate was studied by Fourier transform infrared spectroscopy and circular dichroism. The effect of anthocyanin on the structure of soybean protein isolate was studied by Fourier transform infrared spectroscopy and circular dichroism. The results showed that anthocyanin had strong fluorescence quenching effect on soybean protein isolate in a static mode. The apparent binding constants of anthocyanin and soybean protein isolate at 298K, 306K and 314K were 3.343×104L/mol, 4.507×104L/mol and 5.525×104L/mol, the corresponding binding sites were 0.9178, 0.9546 and 0.9381, respectively. The results of thermodynamic data showed that the interaction between anthocyanin and soybean protein isolate was mainly hydrophobic interaction. Synchronous fluorescence spectroscopy and UV-Vis spectra showed that anthocyanins changed the microenvironment of aromatic amino acid residues in the spatial structure and the conformation of soy protein isolate, and the synchronous fluorescence spectrum showed that the anthocyanin interacted with the tryptophan residue in the soybean protein isolate and reduced the hydrophobic interaction. Fourier transform infrared spectroscopy and circular dichroism showed that the secondary structure of soybean protein was changed by anthocyanin.