Natural phenols are an important functional compound widely distributed in plants with benefits that promote human health. The content of total phenols, flavonoids, and anthocyanins and their composition distribution in 18 soybean cultivars was investigated. There are four phenolic acid distribution forms in these soybean cultivars, namely free, esterified, glycosided, and insoluble-bound. Total phenols, flavonoids, and anthocyanins from 6 black soybean cultivars were found in higher numbers than those from 12 other yellow soybean cultivars. Free and esterified phenolic acids were the main phenolic acid form in all 18 soybean samples. Chlorogenic acid and caffeic acid were the dominant phenolic acids in eight detected phenolic acids, and daidzin and genistin were the abundant isoflavones in five detected isoflavones. Furthermore, the antioxidant activities of total phenols from the 6 black soybean cultivars were greater than those from the 12 yellow soybean cultivars, and there was a significant positive correlation between antioxidant activity and total phenolic content. Black soybeans could be a potential resource for developing natural antioxidants that may play a crucial role in human health protection.