Improper irrigation and fertilization can result in soil compaction, solidification, and acidification, consequently disrupting the equilibrium of the soil microbial community. The objective was to enhance the microbial environment in Panax notoginseng soil, augment bacterial diversity, increase community abundance, and establish a scientific and theoretical foundation for Panax notoginseng cultivation. Panax notoginseng field planting experiment was carried out from 2019 to 2021, involving two controlled variables: irrigation (W) and fertilizer application (F). Three irrigation levels were established, denoted as W1 (0.6 FC), W2 (0.75 FC), and W3 (0.9 FC). A total of 1440 kg•hm−2 of soluble organic fertilizer was applied throughout the entire growth cycle, with varying proportions allocated to each growth stage. Four fertilization levels were designated as F1 (rooting stage: seedling stage: flowering stage: fruiting stage = 25 %: 25 %: 25 %: 25 %), F2 (20 %: 25 %: 30 %: 25 %), F3 (15 %: 30 %: 30 %: 25 %), and F4 (10 %: 40 %: 20 %: 30 %), total 12 treatments. Non-irrigated and non-fertilized CK treatments were employed as control. Soil physicochemical attributes, bacterial diversity, community structure, and functional characteristics across various water and fertilizer treatments were comprehensively assessed utilizing the quotient-weighted TOPSIS method. The results showed that coupled irrigation and fertilization treatments had a significant impact on various soil parameters of Panax notoginseng, including total nitrogen, nitrate nitrogen, ammonium nitrogen, organic carbon, pH, water content, and bacterial alpha diversity (P < 0.05). Moreover, coupled irrigation and fertilization treatments had a highly significant influence on soil water content during the rooting stage, seedling stage, and fruiting stage (P < 0.01). Total nitrogen, nitrate nitrogen, ammonium nitrogen, water content, and pH emerged as the primary environmental factors significantly shaping the structure of the soil bacterial community. In the W2F4 treatment, soil total nitrogen, organic carbon content, pH, Chao1, Shannon index, and functional abundance in categories such as chemoheterotrophy, aerobic chemoheterotrophy, nitrogen fixation, nitrate reduction, nitrogen respiration, and nitrate respiration were notably higher compared to other water-fertilized treatments. Furthermore, the W2F4 treatment ranked first in the TOPSIS comprehensive evaluation. Consequently, the W2F4 treatment emerged as the optimal irrigation-fertilization strategy for enhancing soil microbial activity and fertility in Panax notoginseng cultivation. This study establishes a theoretical foundation for enhancing the microbiological environment of Panax notoginseng soils, augmenting soil bacterial diversity, increasing community abundance, and ultimately elevating soil fertility for the efficient and high-quality cultivation of Panax notoginseng.