Tributyltin (TBT), a recognized endocrine disruptor, is associated with metabolic diseases, including obesity, type 2 diabetes, non-alcoholic steatohepatitis, and osteoporosis. Bile acids (BAs) play pivotal roles in lipid digestion and absorption. However, there are no studies to illustrate the effects of TBT on BA pool composition in circulation. Here, rats were treated with TBT (50 μg/kg) or a vehicle control once every three days for sixty days to analyze serum BA levels using ultra-high-performance liquid chromatography–tandem mass spectrometry (UHPLC-MS/MS). The liver tissue sections and lipid levels of rats were examined using conventional methods. TBT induced sporadic cholestasis in the livers of rats and significantly reduced the levels of five BAs, including four conjugated BAs [acidtaurocholic acid (TCA), taurodeoxycholic acid (TDCA), taurochenodeoxycholic acid (TCDCA), and tauro-β-muricholic acid (Tβ-MCA)] and one unconjugated bile acid [dehydrolithocholic acid (DLCA)], while the serum levels of triglyceride, cholesterol, and bilirubin were unaltered by TBT treatment. These results indicate that TBT exposure affected the BA pool composition in circulation, especially the taurine-conjugated BAs.