Abstract: An ultra-performance liquid chromatography-quadrupole time-of-flight mass spectrometry(UHPLC-Q-TOF/MS)method has been established to analyze the bioactive components of the aqueous extract of Euodiae Fructusand detect the metabolites in rats after oral administration of the aqueous extract. Compounds were detected by analyzing their retention times, high resolution mass data, mass spectra and comparing with the reference substances. As a result, 27 compounds were characterized from the aqueous extract of Euodiae Fructus, and 25 compounds were identified on the basis of the reference substances. 16 parent compounds and 35 metabolites were detected in rats' plasma, urine and feces samples, and all of the parent compounds were determined unambiguously through comparison with the reference substances. Four classes of compounds were identified from the aqueous extract of Euodiae Fructus, including phenolic acids, limonins, flavonoid glycosides and alkaloids. Phenolic acids, flavonoid glycosides and alkaloids were detected in rats' plasma, urine and feces, while limonins were detected in the urine and feces. The main metabolism pathways of these compounds in rats might include hydroxyl, hydrogenation, methylation, sulfating, glucuronidation, and so on. The results of this study provide references in the material basis of Euodiae Fructus in vivo.