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Effects of continuous cropping on rhizosphere soil physical and chemical properties, soil microbial activity, and community characteristics of Codonopsis pilosula were investigated. The C. pilosula plot(CK) fallow for five years and C. pilosula fields with different years of continuous cropping were studied using Illumina high-throughput sequencing technology combined with soil physical and chemical properties analysis. The response of rhizosphere soil physical and chemical properties, microbial activities, and microbial community characteristics to continuous cropping years of C. pilosula were investigated. The results were as follows:the contents of organic carbon, total phosphorus, total nitrogen, and salt in rhizosphere soil of C. pilosula increased with the extension of continuous cropping years. However, soil pH value decreased with the extension of continuous cropping years. Compared with that in the CK treatment, rhizosphere soil organic carbon content of C. pilosula in continuous cropping for one, two, three, and four years increased by 11.1%, 80.5%, 74.9%, and 78.2%, respectively. Total phosphorus content increased by 11.8%, 52.9%, 66.7%, and 78.4%, and total nitrogen content increased by 31.3%, 68.8%, 52.1%, and 56.3%, respectively. Soil salt content increased significantly under continuous cropping of three and four years, and soil conductivity increased by 54.2% and 84.7% compared with that in the CK treatment, respectively. The C/N ratio of microbial biomass in rhizosphere soil exhibited an increasing trend with the extension of continuous cropping years. Soil respiration entropy and microbial entropy showed a decreasing trend. With the increase in continuous cropping years, the diversity and abundance of bacteria in soil decreased, whereas the diversity and abundance of fungi increased. In addition, with the increase in continuous cropping years, the antagonistic effect between bacterial communities was enhanced, whereas the synergistic effect between fungal communities was mainly observed. Correlation analysis showed that soil total phosphorus, available potassium, carbon to nitrogen ratio of microbial biomass, soil respiration entropy, microbial biomass carbon, and electrical conductivity were the main factors affecting the changes in soil bacterial community characteristics. Soil total nitrogen, available potassium, available phosphorus, and soil respiration entropy were the main factors affecting the changes in fungal community characteristics. In conclusion, continuous cropping significantly changed the physical and chemical properties of soil and microbial activity and affected the abundance and diversity of bacteria and fungi in soil. This changed the interaction between microorganisms, which disrupted the stability of microbial communities in the soil.