The objective was to evaluate the interaction between ultrasonic treatment soybean protein isolate and chitosan, and the structural properties of the complexes. The interaction was studied by UV-Vis absorption and fluorescence spectroscopy. The relationships between structure changes and functional properties of soybean protein-chitosan complexes through SDS-PAGE, dynamic light scattering particle size analysis, surface charge and turbidity measurement were investigated. The results showed that with the increase of ultrasonic power, the maximum absorption peak of UV-Vis absorption spectrum was gradually increased and occurred red-shifted;the fluorescence intensity was firstly decreased and then increased. The intensity of the endogenous fluorescence was the highest at 600W. Ultrasonic treatment affected soybean protein isolate subunit composition and mainly promoted the interaction between 7S subunits and chitosan. The particle size of the complex was firstly decreased and then increased. The charge potential of the complexes was larger under 300～500W than those under others. The turbidity was also decreased, which was beneficial to homogeneous distribution and stability of the solution. The results showed that the formation of the complex was relatively stable at low power, but the interaction between soy protein isolate and chitosan was affected by the insoluble aggregation and rearrangement of the protein after high power ultrasonic treatment. The interaction of different complexes affected the microenvironment of amino acid residues, the tertiary structure and molecular flexibility of soybean protein isolate, and then impacted the structure and functional properties of the complexes.