Marein is the main active compound of Coreopsis tinctoria Nutt., and its main activities include antioxidant, hypoglycemic, and hypotensive. After oral administration of marein, the blood concentration of marein is low. The metabolites of marein have not been reported systematically. In this study, a rapid and systematic method based on ultra-high performance liquid chromatography-quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF-MS/MS) was established to detect metabolites of marein in vivo (plasma and urine) after oral administration and injection. Sixty-one metabolites were identified. The metabolites are formed through a wide range of metabolic reactions, including hydroxylation, glucuronidation, methylation, hydrolysis, and desorption of hydrogen. The liver microsome incubation was further used to investigate the metabolic rate of marein. Network pharmacology was applied to study the targets and pathways of marein and its metabolites. Marein and its metabolites act on the same targets to enhance the therapeutic effect. This research illuminates the metabolites and metabolic reaction of marein and establishes a basis for the development and rational utilization of C. tinctoria. Meanwhile, the analysis of prototype and metabolites together by network pharmacology techniques could provide a methodology for the study of component activity.