Abstract: With the extensive use of the antibiotics, especially abuse, the serious problem of bacterial resistance has happened commonly in clinic, and the multi-drug resistant pseudomonas aeruginosa infection has always been the focus and difficulty in clinical anti-infection treatment. After years of clinical trials, it is confirmed that some traditional Chinese medicine have significant antibacterial effect, and can delay or reverse drug resistant in combination with antibiotics. Qi-gui-yin (QGY)，composing of five kinds of traditional Chinese medicine (Astragalus, Angelica Lonicera, Artemisia apiacea, Polygonum cuspidatum), is mainly used for the treatment of multi-drug resistant pseudomonas aeruginosa infection, and is certified to have significant synergistic antibacterial effect with imipenem and ceftazidime. Due to the complexity of chemical composition，pharmacodynamic material basis of QGY is not very clear. In order to futher clarify pharmacodynamic material basis of Qi-gui-yingranule(QGY), HPLC-ESI-LTQ-Orbitrap was used to investigate flavonoids constitutes in serum, urine and feces of rats. In previous studies, the chemical compositions of QGY were analyzed by LC-ESI-MS/MS. By comparing the retention time, accurate molecular weight and MS/MS fragmentation with standards and related literatures, 59 compounds were identified or tentatively characterized in QGY, including flavonoids, phenylpropanoid, anthraquinones, isoflavans, isoflavones, saponins and other compounds. Among them, there were 28 flavonoids with the most types, which suggested that the flavonoids were the major constituents of QGY, and would be the medicinal compositions in treatment of resistance bacterial infection. In this work, the metabolic processes of flavonoids in QGY were mainly studied. 8 flavonoids were identified from medicated serum. Among them, Apigenin-6,8-di-C-glu and Apigenin passed into blood with original structure, while the orther 6 compounds were phase Ⅱ metabolites (formononetin, calycosin, luteolin-7-O-glucoside, kaempferol-3-O-glrcoside, luteolin and 5,7,4′-trihydroxy-flavonol-7-O-β-D-glucopyranoside). 9 flavonoids were identified in urine, 3 compounds in feces. Among them, 6 serum compounds′metabolites were found in urine, including formononetin, calycosin, luteolin-7-O-glucoside, kaempferol-3-O-glrcoside, apigenin and apigenin-6,8-di-C-glu, but no one in feces. The prototype or metabolities of luteolin and 5,7,4′-trihydroxy-flavonol-7-O-β-D-glucopyranoside could not been found in urine and feces, which may be hydrolyzed into small molecular compound in the metabolic process or given off via other metabolic pathways. In this study, it can be found that most of the flavonoids constitutes in serum were excreted through kidney. In sum, the bioactive ingredients in QGY were elaborated preliminarily.