There is a lack of understanding of the dynamic characteristics of carbon, nitrogen, and enzyme activity of soil microbial load of Panax notoginseng in water-fertilizer intercrops. In this study , we reveal that different water and fertilizer regulations affect microbial biomass carbon, nitrogen, and enzyme activities. As the study object, we set up 3 irrigations,4 fertilization levels, and 1 control in micro-sprinkler irrigated Panax notoginseng farmland, Luxi County, Yunnan Province from 2018 to 2020. The findings demonstrated that under the same water and fertilizer management, the carbon, nitrogen, and enzyme activities of Panax notoginseng’s soil increased and then decreased with increasing fertility time, in descending order of flowering, fruiting, seedling, and rooting periods.. The maximum value is reached during the flowering period ,while the minimum value is reached during the rooting period. The soil microbial carbon and nitrogen contents ranged from 0.49 to 1.05 g.kg ^-1 and from 14.98 to 66.21 mg.kg ^-1, respectively, and soil sucrose enzyme activity was the largest, ranging from 17.12 to 68.79 mg.kg ^-1.d. ^-1. The soil microbial carbon , nitrogen and enzyme activities of Panax notoginseng increased with the rate of water and fertilizer application under different water and fertilizer management. The soil microbial carbon , nitrogen and enzyme activities of Panax notoginseng at the flowering period were the largest. The soil microbial carbon and nitrogen activities of Panax notoginseng increased with the increase of irrigation and fertilizer application, whereas the soil microbial carbon and nitrogen activities of W3F4 increased by 0.41 g.kg ^-1 and 39.52 mg.kg ^-1 respectively compared with W1F1. Soil urease, sucrase, acid phosphatase, and catalase activities were the highest in W3F4, with increases of 44.26%, 61.51%, 42.56, and 32.25% respectively compared to W1F1. There was a significant positive correlation between soil microbiomass carbon and nitrogen and enzyme activity under different water and fertilizer management. Soil microbiomass carbon and nitrogen content determined soil enzyme activity. The entropy value method combined with the TOPSIS method was used to analyze the optimal program fit Ci of soil microbial biomass carbon, nitrogen, and enzyme activity under different water and fertilizer optimization management and at different fertility periods. The results showed that the Ci values were F4, F3, F2, and F1 in descending order under the same irrigation level treatment.The Ci values decreased and then increased with increasing irrigation water under the same fertilization level treatment. The carbon, nitrogen, and enzyme activities of the soil’s microbial biomass were successfully controlled when Panax notoginseng was treated with W2F4 during the rooting period and W3F4 during the seedling, flowering, and fruiting periods. This study is an essential guideline for water and fertilizer regulation of Panax notoginseng and its yield quality improvement.