Soybean is highly sensitive to drought stress during its flowering period. Heinong84 (HN84) and Hefeng46 (HF46) were planted in clay loam, silty loam, and sandy clay. We studied the effects of drought stress on the content of membrane lipid peroxides in flowering soybean leaves, the activity of antioxidant enzymes, and the activity of key enzymes of nitrogen metabolism under different soil conditions. Our results showed that soybean had clear physiological responses to drought stress. With increasing drought stress, the malondialdehyde, glutathione reductase, and glutathione peroxidase levels in soybean leaves increased continuously. Superoxide dismutase, peroxidase, glutamine synthase, and glutamate synthase levels increased with drought stress, reaching a maximum under moderate drought stress and then decreased; nitrate reductase activity decreased continuously. Under the condition of sufficient water, the performance of soybean in the three soils is almost the same, but there are differences under drought stress; particularly, soybean grown in clay loam shows the strongest drought resistance. In summary, the physiological state of soybean is easily affected by drought stress, which varies greatly among different cultivars and in different soil types.