Rhodiola crenulata has been widely used as a health food, antifatigue and antidepressant in China and many other countries for centuries. However, to date the metabolism of it in vivo still remains unclear. In this study, UHPLC-FT-ICR MS was used to analyze the major components and their metabolites in rats after oral administration of Rhodiola crenulata for the first time. A total of 179 constituents, including 37 prototype compounds and 142 metabolites (89 phase I metabolites and 53 phase II metabolites) were tentatively identified. The metabolic pathways included hydroxylation, deglycosylation, dehydrogenation, glucuronidation and sulphate conjugation. In summary, this study showed an insight into the metabolism of Rhodiola crenulata in vivo, which may provide helpful chemical information for better understanding the multiple functions of it. And also, the developed method could be used as a reliable strategy to study the metabolic profile for other traditional chinese medicines.