The quality of the same herbal medicines in different daodi-origins in China is significantly different. Our research team previously found that using protocatechuic acid as a chemical marker can divide the Cynomorium songaricum into outside-the Great Wall (Inner Mongolia) and inside-the Great Wall (Gansu). However, the ecological mechanism that causes the quality variation of C. songaricum is unclear. Based on the microbiome-ecological strategy, 16s amplicon sequencing was performed on rhizosphere soils of C. songaricum in two origins (Inner Mongolia and Gansu), and the composition of soil microbial communities was analyzed. Tax4Fun was used to predict the metabolic function of soil microbial communities. Correlation analysis by combing with the abundance of key microbial community and ecological climate factors was performed. Microbiome sequencing results revealed that the diversity of soil microbial communities in Inner Mongolia was significantly higher than that in Gansu. Five core microbiomes (Arthrobacter, Streptomyces, Bacillus, etc.) and six specific biomarkers of soil microbial communities (Microbulbifer, Methyloceanibacter, Cynomorium_coccineum, etc.) which could be distinguished from two origins were identified. For the first time, metabolic function prediction showed the metabolic function profile of soil microbiome of C. songaricum in two origins. Redundancy analysis and correlation analysis results showed that the annual sunshine hours was the main ecological factor affecting the composition of the soil microbial community of C. songaricum, and it was extremely significantly negatively related to Streptomyces and Bacillus. This article provides a new idea for explaining the formation mechanism of quality variation in the daodi-origins of C. songaricum, and also provides a scientific basis for theoretical research on the quality ecology of herbal medicines.