Abstract: Using the soy protein isolate after hydrolysis by pepsin as the substrate to obtain soybean peptides,the effects of secondary structure of soybean protein isolate and soybean peptide on the solubility of soy protein isolate were studied. The structure and microstructure of the two classes were analyzed by infrared spectroscopy and atomic force microscopy. The relationship between structure and function was analyzed by the functional analysis of the changes. The results showed that a-helix and β-sheet of the secondary structure of soybean peptide was 16.38% lower than that of soybean protein isolate,while the β-turn and random coil is about 15.37% higher than one. The surface of soybean peptide was smooth and the particle was dispersed,existing in single molecule state. The particle size was 50% of soybean protein isolate,and the solubility of soybean protein was 4.43 times of that of soybean protein isolate at pH4.0.