Soybean seed products contain isoflavones (genistein, daidzein, and glycitein) that display biological effects when ingested by humans and animals. These effects are species, dose and age dependent. Therefore, the content and quality of isoflavones in soybeans is a key factor to the biological effect. Our objective was to identify the genetic effects that underlie the isoflavone content in soybean seeds. A genetic model for quantitative traits of seeds in diploid plants was applied to estimate the genetic main effects and genotype × environment (GE) interaction effects for the isoflavone content (IC) of soybean seeds by using two years experimental data with an incomplete diallel mating design of six parents. Results showed that the IC of soybean seeds was simultaneously controlled by the genetic effects of maternal, embryo, and cytoplasm, of which maternal genetic effects were most important, followed by embryo and cytoplasmic genetic effects. The main effects of different genetic systems on IC trait were more important than environment interaction effects. The strong dominance effects on isoflavone from residual was made easily by environment conditions. Therefore, the improvement of the IC of soybean seeds would be more efficient when selection is based on maternal plants than that on the single seed. Maternal heritability (65.73%) was most important for IC, followed by embryo heritability (25.87%) and cytoplasmic heritability (8.39%). Based on predicated genetic effects, Yudou 29 and Zheng 90007 were better than other parents for increasing IC in the progeny and improving the quality of soybean. The significant effects of maternal and embryo dominance effects in variance show that the embryo heterosis and maternal heterosis are existent and uninfluenced by environment interaction effects. Soybean seed products contain isoflavones (genistein, daidzein, and glycitein) that display biological effects when ingested by humans and animals. These, content and quality of isoflavones in soybeans is a key factor to the biological effect. Our objective was to identify the genetic effects that underlie the isoflavone content in soybean seeds. A genetic model for quantitative traits of seeds in diploid plants was applied to estimate the genetic main effects and genotype × environment (GE) interaction effects for the isoflavone content (IC) of soybean seeds by using two years experimental data with an incomplete diallel mating design of six parents. Results showed that IC of soybean seeds was simultaneously controlled by the genetic effects of maternal, embryo, and cytoplasm, of which maternal genetic effects were most important, followed by embryo and cytoplasmic genetic effects. The main effects of different genetic sy stems on IC trait were more important than environment interaction effects. Therefore, the improvement of the IC of soybean seeds would be more efficient when selection is based on maternal plants than that On the single seed. Maternal heritability (65.73%) was the most important for IC, followed by embryo heritability (25.87%) and cytoplasmic heritability (8.39%). Based on predicated genetic effects, Yudou 29 and Zheng 90007 were better than other parents for increasing IC in the progeny and improving the quality of soybean. The significant effects of maternal and embryo dominance effects in variance show that the embryo heterosis and maternal heterosis are existent and uninfluenced by environment interaction effects.