The effects of antagonistic Bacillus SXKF16-1 (Bacillus atrophaeu) and SXKF16-2 (B. methylophicus) on the main active components of Astragalus membranaceus var. mongholicus were investigated so as to provide a basis for the development of multi-functional preparations. Healthy A. membranaceus var. mongholicus seedlings were root-irrigated with the fermentation of antagonistic Bacillus, and ten effective components were determined by HPLC-UV-ELSD. There was a good linear relationship (r≥0.9950) in the corresponding linear range of the respective standard curve of calycosin-7-O-β-D-glucoside, ononin, (6aR,11aR)-9,10-dimethoxyptercarpan, 8,2'-dihydroxy-3,4-dimethoxyisoflavan-7-O-β-D-glucopyranoside, calycosin, formononetin, astragaloside Ⅳ, Ⅲ, Ⅱ, Ⅰ, and thus the test results were reliable. Treated with antagonistic Bacillus SXKF16-1 and SXKF16-2, the contents of such A. membranaceus var. mongholicus active components as calycosin-7-O-β-D-glucoside, ononin, (6aR,11aR)-9,10-dimethoxyptercarpan, 8,2'-dihydroxy-3,4-dimethoxyisoflavan-7-O-β-D-glucopyranoside, calycosin, formononetin, astragaloside Ⅱ and Ⅳ showed no significant change, but the contents of astragaloside Ⅰ and Ⅲ increased significantly. Compared with the control group, the content of total flavonoids in the two treatment groups had no significant change, while the content of total saponins increased significantly. Antagonistic Bacillus SXKF16-1 and SXKF16-2 have no negative effect on the content of main active components of A. membranaceus var. mongholicus, and can promote the accumulation of some saponins; and therefore have the potential of being developed into multi-functional preparations.