Abstract: The study aims to screen the ability of the bacteria to metabolize ononin and assess the effect of ononin on the intestinal bacteria. Fresh human fecal sample was obtained from a healthy volunteer, diluted serially in sterile water and sixty-nine different bacterial colonies were picked out ultimately. UPLC-Q-TOF/MS with automated data analysis software (MetaboLynx^TM) was applied to fast analysis of ononin metabolites. Furthermore, an E_max precision microplate reader was employed to determine the growth situation of Enterococcous sp., Enterobacter sp., Lactobacilli sp., and Bifidobacteria sp. Results indicated that hydrogenation, demethylation, hydroxylation and deglycosylation were the major metabolic pathways of ononin by human intestinal bacteria in vitro. Ononin can inhibit the growth of pathogen such as Enterococcus sp., Enterobacter sp. and can promote the growth of probiotics such as Bifidobacteria sp. and Lactobacilli sp. This study suggested that intestinal bacteria have the metabolic effects of ononin and the biotransformation was completed by different bacteria. And ononin can affect the balance of intestinal flora and the degree of influence varies depending on the bacterial species and the concentration of ononin.