The parameters of hydrolysis of soybean isoflavone glycosides catalyzed with complex organic acid were researched by single-factor experiment and orthogonal experiment with hydrolysis rate as the evaluation index. The results showed that the optimal hydrolysis parameters was reaction temperature 135℃, reaction time 160 min, ratio of composite acid (malic acid∶citric acid) 4∶3, hydrolysis rate can reach to above 97.0%. The hydrolysates can be used in health food as raw material without been separated. The hydrolysis process is green environmental protection with application value.