The effects of β-CycloDextrin (β-CD) on three aglycones (daidzein, glycitein and genistein) in soybean milk were investigated by HPLC. The best mobile phase was the mixture of methanol and 5% acetic acid glacial (40:60, V/V). It was found that adding 1% of β-CD into soybean milks could increase the thermal stabilities of the three aglycones. The contents of daidzein, glycitein and genistein in soybean milk containing β-CD were 8.89%, 13.81% and 9.75% respectively higher than those in soybean milks without of β-CD after incubated at 95 ℃ for 10 min, were 9.59%, 8.77% and 2.45% respectively higher than those in soybean milks without of β-CD after incubated at 121 ℃ for 1min and were 8.90%, 11.92%, and 6.69% respectively higher than those in soybean milks without of β-CD after incubated at140 ℃ for 10 s.