Abstract: Through pot and hydroponics experiments of wheat/faba-bean, mono-cropped faba-bean and mono-cropped wheat, soy isoflavone exudate of faba-bean and wheat were studied under different nitrogen (deficient, adequate and excessive) conditions at different growth stages. The study aimed at providing the basis for further understanding of yield increase and disease control mechanisms of intercropping systems. The results showed that with the growth of crops, soy isoflavone exudate of wheat roots decreased, while that of faba-bean first increased before decreased. With the increase of nitrogen application rate, soy isoflavone exudate of both wheat and faba-bean decreased, and most changes were significant. Compared with deficient nitrogen treatment, soy isoflavone exudates of intercropped wheat were increased respectively by 18.9% and 122.1% at stem elongation stage (60 d after sowing) under adequate and excessive nitrogen conditions. Accordingly, soy isoflavone exudate of mono-cropped wheat was increased by 28.9% and 72.7% under adequate and excessive nitrogen conditions. Crops intercropping increased soy isolavone secretion of crops, which was significant only at lower nitrogen level. Compared with mono-cropped wheat under deficient and adequate nitrogen condition at stem elongation stage of wheat (60 d after sowing), soy isoflavone exudate of intercropped wheat was significantly increased by 26.9% and 12.0%, respectively, in pot experiment, and 15.3% and 59.2% in hydroponics. Compared with mono-cropped faba-bean under deficit and adequate nitrogen rates at branching stage (60 d after sowing), root soy isoflavone secretion of intercropped faba-bean was significantly increased by 64.6%, and 11.4% in pot experiment, and 23.8% and 14.1% in hydroponics experiment, respectively. At flowering and filling stages of wheat, and flowering and pod-bearing stages of faba-bean, the similar tendency was observed. In short, both intercropping and nitrogen fertilization changed root secretion of soy isoflavone by wheat and faba-bean, which was more obvious under lower nitrogen application rate.