Swertia mussotii Franch. (SMF), a rare Tibetan medical plant in China, is renowned as one of the "Eight Precious Tibetan Medicines". It plays an important role in treatment of jaundice hepatitis and other diseases due to its remarkable clinical efficacy. The multiple bioactive components it contains have been proven to exhibit a wide range of pharmacological effects. The purpose of this study was to investigate the components and metabolic processes of SMF. UPLC-Q-TOF-MS/MS technology was used to analyze the main components of SMF, and metabolites of the extracts were detected in bile, serum, urine and feces of rats after oral administration. Meanwhile, the pharmacokinetic parameters of seven bioactive constituents (swertiamarin, sweroside, gentiopicroside, loganic acid, isoorientin, isovitexin, and mangiferin) were quantitatively determined using triple quadrupole LC-MS/MS. The results showed that 11 compounds, including iridoid glycosides, flavonoids and triterpenoids, were identified from SMF extracts. In the biological samples, a total of 11 prototype components and 59 metabolites were detected. The pharmacokinetic analysis of 7 main components showed that the blood concentration of iridoid glycosides were significantly higher than those of other components, and tmax of all components was prolonged except gentiopicroside. This study provides a systematic clarification of the metabolic characteristics and pharmacokinetic profile of SMF, offering a scientific foundation for evaluating its clinical safety and efficacy.