In order to obtain a higher content of soybean isoflavone glycosides and improve the flavor of soybean milk, two kinds of glycosidase (R.B1L and R.CL) were used in soybean milk processing, then the soybean isoflavones and lavor compounds were detected by high performance liquid chromatography (HPLC) and gas chromatography-mass spectrometry technique(GC/MS) respectively. The results showed that the amount of soybean isoflavone aglycones increased 7.289 μg/g, which was 35.7% higher than the control group. While, the bean flavor compounds of hexanal and 2-amyl furan decreased 10.8%, and the aroma compounds of hexyl alcohol and anti-2-nonene aldehyde increased 10.88%. It indicates that the glycosidase can provide a good method for improving the quality and flavor of soybean milk.