Abstract: OBJECTIVE To explore the difference of some alkaloids in Coptidis Rhizoma - Mume Fructus decoction and Xiaoai Jiedu Prescription， and compare their effects on the intestinal flora of mice. METHODS The separation was performed on Extend-C₁₈ column (100 mm×2.1 mm， 1.8 μm) with 0.1% aqueous formic acid (A)-acetonitrile solution (B) as the mobile phase for gradient elution. The flow rate was 0.3 mL/min， column temperature was set at 35 ℃， and injection volume was 2 μL. Electrospray ionization source was applied for the analysis under positive ion model. The method was validated and the samples were determined under this condition. 50 mice were divided into ZC group， QFH group， QFL group， YDH group and YDL group according to different dosages. After 7 days of oral administration， fecal samples from each group were collected for 16S rRNA gene sequencing. RESULTS The established detection method showed good linearity within certain concentration ranges and the method validation results meet the relevant requirements. The contents of magnoflorine and columbamine in the single herb， herb pair and formula decoction were （4.433±0.133） and （8.905±0.154） mg/g， （3.545±0.033） and （9.170±0.051） mg/g， （5.287±0.038） and （13.861±0.690） mg/g， respectively. In addition， the abundance of Bacteroides in QF and YD were higher than that in the normal group， but the abundance of Firmicuteswas opposite. Interestingly， we found that the abundance of Verrucomicrobia and Proteobacteria in YDH were higher than other groups. CONCLUSION The method and related parameters were simple and reliable， which could be used to detect the content of related components. Compared with single herb， the content of columbamine was increased both in herb pair and Xiaoai Jiedu Prescription; the content of magnoflorine was decreased slightly in herb pair， while increased in Xiaoai Jiedu Prescription. After administering herb decoction， the change of intestinal flora diversity revealed Coptidis Rhizoma - Mume Fructus decoction and Xiaoai Jiedu Prescription could regulate the balance of intestinal system. The results further explain the compatibility mechanism of the two drugs in this prescription.