Panax notoginseng is a prominent traditional Chinese medicinal herb, yet its yield and quality are significantly constrained by continuous cropping obstacles, primarily stemming from soil-related issues. This study analyzed soils subjected to various degrees of continuous P. notoginseng cultivation, soils without P. notoginseng planting, and natural forest floor soil without P. notoginseng planting. The objective was to investigate variations in soil microbial communities, physicochemical properties, and enzyme activities across different cropping conditions. Macro-genome sequencing was employed to reveal microbial shifts and key factors influencing rhizosphere microbial communities. Notably, the natural forest floor soil exhibited the highest levels of soil organic matter, soil organic carbon, total nitrogen, and available potassium. Furthermore, continuous cropping soils showed the highest levels of pH, available phosphorus, electrical conductivity, and total potassium. The activities of catalase, urease, acid phosphatase, sucrase, and soil FDA hydrolase decreased significantly after continuous cropping, but increased again after five years of fallowing. Microbial analysis revealed that Bacteroidetes, Firmicutes, and Chloroflexi dominated the soils without P. notoginseng planting, whereas Proteobacteria, Actinobacteria, and Acidobacteria were the predominant phyla in continuous cropping and natural forest floor soils. Continuous cropping led to an increase in Acidobacteria, Gemmatimonadetes, and Chloroflexi, while fallowing reduced Actinobacteria. Gemmatimonades was almost exclusively present in the continuous cropping soils. Overall, continuous P. notoginseng planting altered the soil nutrients and microbial composition. Key factors influencing microbial communities included pH, nitrate nitrogen, available phosphorus, available potassium, and electrical conductivity. The study suggests that attention should be paid to scientific and rational fertilization practices to mitigate the effects of continuous cropping. Additionally, a fallow period of more than five years is recommended. The proper application of probiotic fertilizers is also advised. Finally, cultivating P. notoginseng under forest conditions is recommended as a viable method.