Nitrogen and sulfur are major elements influencing plant growth and production of secondary metabolites. They interact to each other, but little is known about it in Isatis indigotica Fort. plants. In this study, 15 different treatments representing all possible combinations of 3 N treatments (N1, N2, and N3, corresponding to 5, 15, and 25 mM N, respectively) and five S treatments (S0, S1, S2, S3, and S4, corresponding to 0.00, 1.25, 2.50, 5.00 and 7.50 mM S, respectively) were used, and plant growth, indigo and indirubin yields, and expressions of genes encoding enzymes involved in N and S metabolisms were measured. The results show that the highest dry biomass was observed in N2S2 treatment. Moreover, net photosynthetic rate in the N2S2 treatment was significantly higher than under other treatments (except for N3S2 treatment). A low nitrogen concentration (5 mM) was beneficial to the accumulation of alkaloids, and the N1S1 and N2S2 treatments resulted in the highest yields of indigo and indirubin, respectively. Additionally, the yields of indigo and indirubin were positively correlated with the expression of APS reductase and glutamine synthetase genes, respectively.Additional key words: indigo, indirubin, photosynthetic rate, RT-qPCR, stomatal conductance, transpiration rate.