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The cultivation of Panax notoginseng has been plagued by a multitude of challenges, including recurrent diseases, suboptimal value, inadequate quality, and environmental degradation resulting from improper water and fertilizer management. To address these issues and improve the yield of P. notoginseng and its saponin content, this study endeavors to identify the optimal irrigation and fertilization levels in shaded environments in Yunnan Province in Southwest China. In this field experiment, three-year-old plants were tested to evaluate the effects of water, soluble organic fertilizers, and their combinations on plant growth, physiological parameters, yield, and saponin content. The experiment included 12 treatments with three types of irrigation (10 (W1), 15 (W2), and 20 (W3) mm), totaling 440, 660, and 880 mm, and four levels of the total amount of fertilization (F1 (60, total N 12.6, total P 5.5, and total K 10.5 kg ha−1), F2 (90, total N 18.9, total P 8.3, and total K 15.7 kg ha−1), F3 (120, total N 25.2, total P 11.0, and total K 20.9 kg ha−1), F4 (150, total N 31.5, total P 13.8, and total K 26.1 kg ha−1)). The randomized complete block design was used, with 36 plots in total and 3 replications. The study utilized the TOPSIS method to determine the most effective water and fertilizer management strategy for the growth and production of P. notoginseng. The assessment of yield, water and fertilizer productivity, and saponin content across all treatments revealed that the W3F3 treatment resulted in significant increases in the plant's height, stem diameter, and net photosynthetic rate. Meanwhile, the W2F3 treatment exhibited the best root morphological traits. The W3F4 treatment effectively increased dry matter and transpiration. The combination of water and fertilization had a coupling effect that not only increased yield to 1400 kg ha−1 but also improved water–fertilizer productivity. The application of the W2F3 treatment resulted in a significant increase in the accumulation of active components, leading to a total P. notoginseng saponin (PNS) content of 24.94%. Moreover, the comprehensive index obtained through the TOPSIS model indicated that the W2F3 treatment outperformed other treatments. Therefore, this treatment can be considered a promising water and fertilizer model for P. notoginseng cultivation, which can enhance its yield, quality, and productivity while promoting sustainable green development. [ABSTRACT FROM AUTHOR]