ABSTRACT: Soybean cyst nematode (SCN, Heterodera glycines) is a chief plant–parasitic nematode of soybean. Application of synthetic chemical nematicides poses negative side effects to human health and the environment. Therefore, the search for a safe and effective approach is more relevant. This study evaluated the effects of Genistein and Daidzein on the physiological index of soybean cyst nematodes, individual morphology, reversal frequency, respiration, and body fluid leaking of second–stage juveniles (J2s) of soybean cyst nematode. The results showed that body length of J2s decreased, while stylet and tail transparent area elongated. Additionally, after the treatment, the body became hollow and shrunken, the J2s stiffened, whereas the reversal frequency decreased dramatically after 24 h of treatment. Moreover, the body fluid leakage was intensified and respiration was inhibited. Oxygen consumption decreased by 86.7 % and 70.1 %, while, in contrast, electrical conductivity increased by 40.1 % and 36 % at 100 μg mL−1 of Genistein and Daidzein, respectively, after 48 h of exposure. The smaller number of J2s in soybean roots, the slower development rate, and the abnormal sexual differentiation were found in greenhouse assay. Thus, Genistein and Daidzein, especially Genistein, have strong effects on the physiological index of soybean cyst nematodes. Moreover, the effects were time and dosage–dependent.