Rhizoma coptidis has been used for a long time in China owing to its anti‐bacterial, anti‐diabetes, anti‐hyperlipidemia and anti‐obesity activities. However, the in vivo biotransformation of Rhizoma coptidis is still unclear to date. In this study, a three‐step strategy using UPLC‐Q‐TOF/MS was applied to clarify the in vivo absorbed constituents and metabolites in rats after oral administration of Rhizoma coptidis. First, alkaloids in Rhizoma coptidis extract were identified. Second, six abundant alkaloids (berberine, palmatine, coptisine, epiberberine, jatrorrhizine, and columbamine) were selected as representative prototypes and the metabolic fates of them in rats were investigated to obtain a database of Rhizoma coptidis‐derived metabolites. Finally, the metabolic profiles of Rhizoma coptidis were fully elucidated based on the above‐mentioned results. In summary, 29 alkaloids were identified in Rhizoma coptidis, and a database of Rhizoma coptidis‐derived metabolites was obtained with 144 characterized metabolites. A total of 89 xenobiotics including 12 absorbed constituents and 77 metabolites were identified in dosed rat biosamples. Major metabolic pathways of Rhizoma coptidis were hydroxylation, reduction, methylation, demethylation, demethylenation, desaturation, glucuronidation and sulfation. This is the first systematic study on the in vivo absorbed constituents and metabolic profiling of Rhizoma coptidis and will be beneficial for its further studies.