Traditional Chinese medicine (TCM) has been widely used in many oriental countries for thousands of years and played an indispensable role in the prevention and treatment of diseases, especially the complicated and chronic ones. It is a very complex mixture containing hundreds or thousands of different components. Pharmacokinetic study on active constituents in TCM preparations is a good way for us to explain and predict a variety of events related to the efficacy and toxicity of TCM. A selective and sensitive method of ultra performance liquid chromatography coupled with electrospray ionization/quadrupole-time-of-flight mass spectrometry (UPLC-ESI-Q-TOF-MS/MS) was first developed to screen the potentially bioactive components in vivo, using the semi-quantitative determination of multicomponents in the rat plasma after a single oral administration of Yin-Chen-Hao-Tang (YCHT), a famous TCM formula for liver disorders. Hierarchical cluster analysis (HCA) and principal component analysis (PCA) were built to evaluate the differences of pharmacokinetic behaviors (time-course) of the absorbed components of YCHT. Here, we report that the developed method was successfully applied to monitoring the pharmacokinetic time-course of 21 compounds in rat plasma, and were grouped in 3 separate clusters using pattern recognition approaches (both HCA and PCA). Comparing the body dynamics of each composition, the initial choice of the following 9 compounds as the candidate components was: 7-methoxycoumarin-6-hydroxyl sulfate, genipingentiobioside, geniposide, 6,7-dimethylesculetin, peak 16, chimaphylin, 6-dementhoxycapillarisin, capillarisin, rhein. Pharmacokinetics based-UPLC-ESI-Q-TOF-MS/MS combined with HCA and PCA approaches can provide a reliable and suitable means of identifying and screening potentially bioactive components contributing to pharmacological effects of TCM, further prospecting natural products in the search for new leads in drug discovery.