This study compared the growth and flavonoid accumulation of Astragalus membranaceus var. mongholicus from Wengniute Banner, Chifeng City, Zhenglan Banner, Xilin Gol League and Guyang County, Baotou City of Inner Mongolia Autonomous Region, Hunyuan County, Datong City, Shanxi Province, and Luxi County, Dingxi City, Gansu Province, and analyzed the rhizosphere soil microorganisms by Illumina MiSeq highthroughput sequencing in different growth stages. The results showed that: (1) during growth period, the A. membranaceus var. mongholicus in Guyang, Hunyuan and Chifeng grow faster, root dry weight peaked in September, there was little difference between provenances of other biomass indicators. (2) The content of calycosin7Oβglucoside in the roots of Longxi and Hunyuan provenance was higher and peaked in September. Other components (ononin, calycosin and formononetin) were fluctuating. (3) There was a great influence on the microbial community in the rhizosphere soil at different growth stages of A. membranaceus var. mongholicus. The rhizosphere bacteria had the most obvious influence which the diversity was higher in September, and the difference in fungal communities was relatively small. While the rhizosphere microbial community composition was similar among different provenances. This study showed that the content of calycosin7Oβglucoside of A. membranaceus var. mongholicus was significantly increased during the growth period, so the best harvest period should not be too early. And the difference of microbial community structure may be one of the important factors for obtaining growth advantage and accumulation of active constituents of A. membranaceus var. mongholicus.