Abstract: In our previous study, it has been confirmed that the 50% ethanol extract of Euodiae Fructus is a hepatotoxic active part, and its metabolism in rat serum has been revealed. However, the metabolic pathway of traditional Chinese medicine in vivo is multiple. A diverse analysis for the metabolism behavior of components will provide us a deep understanding for the qualitative metabolic law and action process in vivo between prototype components and metabolites. In this study, ultra-high performance liquid chromatography-quadrupole-time of flight mass spectrometry (UPLC-Q-TOF MS) was used to detect chemicals in rat bile, urine and feces after administration of Euodia rutaecarpa (35 g/(kg·d)) once a day for fourteen consecutive days. By comparing the BPI chromatograms of samples in positive and negative ion modes, it was found that the response signals in negative ion mode were all responsive in positive ion mode, and the response was better. So the positive ion data was selected for the subsequent analysis. The BPI chromatograms of blank bile and medicated bile, blank urine and medicated urine, blank feces and medicated feces were compared and analyzed. A total of 10 components in bile, 20 components in urine and 26 components in feces were detected. Further comparison with the retention time and mass spectrum data of chemical components in the hepatotoxic part of Euodiae Fructus showed that there were 4 prototypes in bile, 15 prototypes in urine and 22 prototypes in feces. By positive ions MSE scanning mode, the data of compounds with mass range of 50-1 200 u were collected. Through comparing with the database with UNIFI software, the retention time of each component, accurate information, primary and secondary mass spectrometry combined with compound cracking rule and existing literature reports, 29 compounds were identified, including 23 prototype components and 6 metabolites. Further, the possible metabolic pathways were deduced by reversely tracing the prototype components of the metabolites. The main metabolic pathways of these components in vivo include glucuronide binding, sulfation, formylation, hydroxylation and demethylation and so on. The metabolism and excretion process in vivo were further revealed by comparing the distribution of prototype components and metabolites in different biological samples. The main existing forms and metabolic pathways of Euodiae Fructus in rat bile, urine and feces were clarified, which provided a valuable reference for revealing the hepatotoxic substances and metabolism law of Euodiae Fructus. At present, the metabolites identification of traditional Chinese medicine is limited to the metabolites with literature reports and prior knowledge. And the results are not very reliable only by analysis of chromatography and mass spectrometry. It is necessary to verify the meaningful metabolites by nuclear magnetic resonance and other methods in the future research to get the exact conclusion.