In pursuit of maximum yield and economic benefits of Panax notoginseng, farmers usually apply excessive fertilizer and irrigation. Which easily induce the decline of Panax notoginseng quality, fertilizer and water use efficiencies and soil health. From 2021–2023, a field experiment was conducted in Dali Village, Luxi County, Honghe Prefecture, Yunnan Province, to study the response of soil microbial community, root nutrient content, and ginsenoside content of Panax notoginseng to different water and fertilizer regulation. The experiment including three irrigation levels (F1: 120 mm, F2: 240 mm, and F3: 360 mm) four fertilization rates(F1: 48 kg ha−1, F2: 72 kg ha−1, F2: 96 kg ha−1, and 120 kg ha−1),and a CK treatment (no fertilizer and no irrigation) The results showed that the average N, P, and K contents across all treatments were greater in 2023 than those in 2021 and 2022. W3F4 treatment significantly increased N absorption. W2F4 treatment significantly increased P and K absorption. W2F4 treatment significantly increased the Panax notoginseng yield, and W3F2 treatment significantly increased the saponin content. The Panax notoginseng yield ranged from 1165 to 3006 kg∙ha−1, with a maximum average yield in 2023. The Re content averaged 81.5 % in 2023 over 2021, and the highest Re content in W3F2 treatment in 2023 was 108.54 mg∙g−1. In 2023, W2F3 treatment had the highest R1 content of 15.34 mg∙g−1, W2F3 treatment had the highest content of Rg1 of 44.65 mg∙g−1, and W3F2 treatment had the highest Rb1 content of 52.52 mg∙g−1. From 2021–2023, the total number of unique OTUs in W1F1 was the largest, out followed by W3F2, W3F4, and W3F1. The treatment that significantly increased the bacterial Chao1 index was W3F1 and W2F2 in 2021, W3F3, W2F1, W2F1 and W2F3 in 2022, and W2F3 and W2F4 in 2023. The Shannon nor Simpson indices were not varied significantly from CK. At the phylum level, W1F3 in 2021 and W3F1 in 2022 and 2023 improved the relative abundance of Proteobacteria, Acidobacteriota At the genus level, W1F1 in 2021 and 2023 improved the relative abundance of Vicinamibacteraceae_norank and Vicinamibacterales_norank. LEfSe analysis of soil microbial communities showed the most divergent species in 2021 with W3F2, W1F1 in 2022, and W2F1 in 2023. Different water and fertilizer treatments affected the total OTU number of bacterial communities and changed the bacterial community structure. W3F1 and W2F3 treatments significantly increased soil bacterial diversity, and soil microbial diversity regulated plants N as well as R1 and Rg1 content, and the quality of Panax notoginseng is related to microbial diversity. N, P, K, and R1 had a significant positive correlation with microbial community diversity (P<0.05). The W1F1 treatment communities were relatively abundant, and the community species showed high similarity in W3F1 and W2F3.