Abstract: This study was designed to determine the metabolites of Renduining injection in rats. The ultra-high performance liquid chromatography-LTQ Orbitrap mass spectrometric (UHPLC-LTQ-Orbitrap-MS) and mass defect filter techniques were applied to analyze the metabolites of Reduning injection in rat plasma, bile, urine and feces. As a result, we determined 14 metabolites of geniposide, including oxidation, dehydration, hydroxymethylene loss, hydrolysis, ring-opened, cysteine conjugation and glucuronidation conjugation of aglycone; 9 metabolites of geniposidic acid, consisting of dehydration, ring-opened, double-bond reduction and cysteine conjugation; 6 metabolites of secoxylogain including hydrolysis, hydroxymethylene loss, hydroxylation and ethylation; 12 metabolites of chlorogenic acid, containing decarboxylation, hydrolysis, methylation, acetylation, cysteinylglycine conjugation and glutathione conjugation. It provided information for the therapeutic effect of Reduning in vivo.