ETHNOPHARMACOLOGICAL RELEVANCE: Scutellaria baicalensis (S. baicalensis) is the root of S. baicalensis Georgi. In traditional Chinese medicine it is divided into Tiaoqin (TQ, 1-3 years old) and Kuqin (KQ, more than 3 years old). However, the differences in TQ and KQ efficacy and their exact mechanisms are still unclear. AIM OF THE STUDY: This study aimed to clarify the difference in the efficacy of TQ and KQ in relation to different fever types (damp heat and hyperpyrexia) by using rat models, as well as to determine the primary molecular mechanism. MATERIALS AND METHODS: This study compared the compositional content of TQ and KQ by UPLC-MS/MS. Then, rat models of hyperpyrexia (HP, LPS) and damp heat (DH, high-fat and high-sugar diet feeding + fumigation in artificial climate chamber + E. coli injection) were established and their clinical symptoms, blood biochemistry, histopathological sections, cell cytokines and protein expression were compared following treatment with TQ or KQ. Finally, the mechanisms underpinning the differences observed for TQ and KQ were determined by measuring the components of these treatments in different target organs. RESULTS: This study identified 31 compounds in the water extracts of both TQ and KQ, which differed significantly in their relative content. TQ and KQ showed different functional tropism in HP and DH model rats. Baicalin, wogonoside, oroxin A, baicalein, wogonin and oroxylin A appeared to be the basic functional components responsible for the functional tropism hypothesis, while the remaining compounds appeared to be the efficacy-oriented components. In addition, the difference in pharmacodynamics between TQ and KQ may be related to their absorption in vivo, which was consistent with the hypothesis of functional tropism proposed in this work. CONCLUSION: In this study we adopted TQ and KQ-different specifications of Scutellaria baicalensis with similar chemical components-as a case study to systematically reveal the functional tropism of Chinese herbal medicine (CHM). The results showed that TQ and KQ contain the basic functional components to enable the basic function of 'clearing heat', while the variation in compositional content may result in their different therapeutic effects. A greater understanding and utilisation of the functional tropism of CHM would enormously improve the accuracy and scientific basis for the application of CHM medication, as well as in promoting the multi-function mechanism of CHM and guiding new drug development of CHM.