The isoflavone content of 8 different soybean samples was analyzed by HPLC/MS in this paper. The results showed that genistin(G) and malonygenistin (MG) are two major isoflavone species in all samples, and the content accounted more than 50% of total isoflavone content. The total content of Daizine (D) and malonygenistin (MD) ranked next to them, accounting about 38% of total isoflavone. Glycitin(GL) and malonyglycitin (MGL) had very low content in all samples, accounting about 68% of total isoflavone content. The big size soybean, such as yellow soybean, had higher total isoflavone content than both black soybeans and qing soybeans, while small size soybeans had higher total isoflavone content than big size soybeans. DPPH and FRAP results showed that black soybeans had higher antioxidant capabilities than yellow and qing soybean. And small size soybeans had higher antioxidant capabilities than big size soybeans.