To address the prevailing problems of high water and fertilizer input and low productivity in Isatis tinctoria L. production in the Hexi Corridor in China, the effects of different irrigation amounts and nitrogen application rates on growth characteristics, photosynthetic physiology, root yield, and quality of I. tinctoria plants were studied with the aim of obtaining the optimal irrigation level and nitrogen application rate. From 2021 to 2023, we established a two-factor split-plot experiment in the oasis irrigation area with three irrigation amounts (sufficient water, medium water, and low water are 100%, 85%, and 70% of the typical local irrigation quota) for the main zone; three nitrogen application rates (low nitrogen, 150 kg ha−1, medium nitrogen, 200 kg ha−1, and high nitrogen, 250 kg ha−1) for the secondary zone; and three irrigation amounts without nitrogen as the control to explore the response of these different water and nitrogen management patterns for I. tinctoria in terms of growth characteristics, photosynthetic physiology, root yield, and quality. The results showed the following: (1) When the irrigation amount was increased from 75% to 100% of the local typical irrigation quota and the nitrogen application rate was increased from 150 to 250 kg ha−1, while the plant’s height, leaf area index, dry matter accumulation in the stem, leaf, and root, as well as the net photosynthetic rate (Pn), the stomatal conductance (Gs), and the transpiration rate (Tr) of I. tinctoria increased gradually, and the root–shoot ratio decreased. (2) When the irrigation amount increased from 75% to 100% of the local typical irrigation quota, the yield and net proceeds of I. tinctoria increased from 43.12% to 53.43% and 55.07% to 71.61%, respectively. However, when the irrigation quota was 100% of the local typical irrigation quota, and the nitrogen application rate increased from 150 to 200 kg ha−1, the yield of I. tinctoria increased from 21.58% to 23.69%, whereas the increase in nitrogen application rate from 200 to 250 kg ha−1 resulted in a decrease in the yield of I. tinctoria from 10.66% to 18.92%. During the 3-year experiment, the maximum yield of I. tinctoria appeared when treated with sufficient water and medium nitrogen, reaching 9054.68, 8066.79, and 8806.15 kg ha−1, respectively. (3) The effect of different water and nitrogen combination treatments on the root quality of I. tinctoria was significant. Under the same irrigation level, increasing the nitrogen application rate from 150 to 250 kg ha−1 could increase the contents of indigo, indirubin, (R,S)–goitrin, total nucleoside, uridine, and adenosine in the root of I. tinctoria from 3.94% to 9.59%, 1.74% to 12.58%, 5.45% to 18.35%, 5.61% to 11.59%, 7.34% to 11.32%, and 14.98% to 54.40%, respectively, while the root quality of I. tinctoria showed a trend of first increasing and then decreasing under the same nitrogen application level. (4) AHP, the entropy weight method, and the TOPSIS method were used for a comprehensive evaluation of multiple indexes of water–nitrogen coupling planting patterns for I. tinctoria, which resulted in the optimal evaluation of the W3N2 combination. Therefore, the irrigation level was 100% of the local typical irrigation quota, the nitrogen application rate should be appropriately reduced, and controlling the nitrogen application rate at the level of 190.30–218.27 kg ha−1 can improve water–nitrogen productivity yields for I. tinctoria and root quality. The results of this study can provide a theoretical basis and technical support for a more reasonable water and fertilizer management model for the I. tinctoria production industry in the Hexi Corridor in China.
