Abstract Codonopsis pilosula (Franch.) Nannf. is an essential traditional medicinal herb in China. Soil sickness caused by continuous cropping is the main reason for the yield reduction of C. pilosula . However, because of the lack of systematic research on the mechanism of continuous cropping obstacles in C. pilosula , there is a lack of effective measures to reduce or even restrain the disorder of continuous cropping obstacles in C. pilosula . The root system, inter‐root soil microorganisms and non‐inter‐root soil of C. pilosula under a continuous cropping system (e.g. crop rotation, two consecutive crops and three consecutive crops) as well as under different mulching methods (the mulched film and the uncovered) were used as experimental materials for the study. The plant growth of C. pilosula was significantly inhibited when continuous cropping reached 2 years. At the same time, the mulched film significantly ( p < .05) promoted the development of C. pilosula under continuous cropping and considerably mitigated the plant death rate of C. pilosula in all fields. The content of soil nutrients, such as organic matter and inorganic nitrogen, decreased with increasing years of continuous cropping. In contrast, the mulched film improved this soil nutrient in continuous cropping. There was a tendency for the number of endemic operational taxonomic units (OTUs) to decrease in continuous cropping. Additionally, the mulched film altered the distribution of shared and endemic OTUs in the samples and had a recruiting effect on inter‐root microorganisms in continuous cropping. Betaproteobacteriales flora abundance decreased with increasing years of continuous cropping, which showed a strong positive correlation with the immune system and environmental adaptation function. The mulched film increased the abundance of beneficial microorganisms, such as AKAU4049 , Betaproteobacteriales and Gaiellales , to adapt and improve the continuous crop disorder of C. pilosula . In conclusion, mulching can enhance the soil environment and facilitate the growth and development of C. pilosula during continuous cultivation.