As one of the secondary metabolites, the isoflavones formed during the development of soybean [Glycine max (L.) Merr.] seeds. The total and individual isoflavone contents, a typical quantitative trait, were affected by significant genotypes of environments (GE) interaction and controlled by many genes with main or minor effects. In the present study, 99 soybean cultivars, collected from northeast China, were used to analyze the isoflavone performances. Genotype-genotype×environment (GGE) biplot software demonstrated an ability to provide information on genetic main effects than solely on phenotypic perform. High-performance liquid chromatography (HPLC) system was used to extract and determine the isoflavone contents. The results indicated that most genotypes significantly varied among six tested environments. P40 (Xiaolimoshidou) was the best-performed genotype with mean performance and stability for glycitein content across six different environments. P88 (L-59Peking) was the super genotype with mean performance and stability on each tested environment for daidzein, genistein and the total isoflavone. E5 (Gongzhuling in 2016) was the best environment for optimal environmental factor mining. P70 (Charleston), P67 (Baichengmoshidou) and P50 (Jiunong 20) were the optimal genotypes with the highest field among 99 cultivars on each tested environment for genistein. P70 (Charleston), P67 (Baichengmoshidou) and P14 (Hefeng 25) were the optimal genotypes with the highest field among 99 cultivars on each tested environment for daidzein. P40 (Xiaolimoshidou), P45 (Jinshanchamodou), P33 (Dongnong 48) and P56 (L-5) were the optimal genotypes with the highest field among 99 cultivars on each tested environment for glycitein. P70 (Charleston) and P67 (Baichengmoshidou) were the optimal genotypes with the highest field among 99 cultivars on each tested environment for the total isoflavone. GGE biplot was a rational method for stability and adaptation evaluation of soybean isoflavones, and could assist soybean breeder to select a good culture and a suitable tested site. It provided a scientific basis for the establishment of a breeding site and a selection site of soybean isoflavones. This study was valuable to identify genotypes with stable performances of isoflavones of these 99 cultivars for developing new cultivars.