Swertia cincta, a plant of the genus Swertia in Gentianceae, has "heat-clearing" and detoxifying effects that normalize the gallbladder function in the treatment of jaundice. Although numerous studies on Swertia cincta have been performed, the absorption and pharmacokinetic behaviors remain unclear. In this study, the compounds of Swertia cincta in serum, bile, feces, and urine of rats were analyzed using a ultra-high-performance liquid chromatography-tandem mass spectrometry. A total of 9 prototype components and 48 metabolites were detected in biological samples. Furthermore, we determined the main components absorbed in the blood of Swertia cincta and established a method for simultaneously determining these components (sweroside, swertiamarin, and gentiopicroside) in positive ionization mode within 6 min. The quantitative method was successfully applied for the multiple-component pharmacokinetic study of Swertia cincta.