Objective To study the effects of intrahepatic cholestasis on intestinal bile acid metabolism and intestinal flora，and to lay the groundwork for further revealing the effect of intrahepatic cholestasis on the body and its mechanism. Methods Twenty male BALB/C mice were divided into model group and normal group，with 10 mice in each group. Based on multiple reaction monitoring（MRM）⁃based targeted metabolomics，the effect of intrahepatic cholestasis on 33 bile acids in the intestines of mice was analyzed，and the changes of intestinal flora in ileum and colon were detected by high ⁃throughput sequencing. Results There was a great difference in the distribution of bile acid spectrum between the two groups. Primary bile acids such as CA，UDCA and TCA were enriched in the model group，while secondary bile acids such as HDCA，GLCA，THDCA and TLCA were enriched in the normal group. The difference was statistically significant. Compared with those in the normal group，the abundance and diversity of colonic flora in the model group were significantly decreased，while those in the ileal segment were significantly increased. There were significant differences in flora between the two groups. In the normal group，probiotics such as Roseberg，Butyricicoccus，Mucispirillum and other probiotics were dominant，while cholhalophilic bacteria and Toona sinensis were dominant in the model group. Conclusion Intrahepatic cholestasis has an effect on bile acid spectrum of ileocecum in mice，and the secondary bile acids such as HDCA and GLCA are significantly decreased，which may be related to the weakening of intestinal barrier function and the changes of intestinal flora.