The purpose of this study was to establish a chemical profiling method to compare the chemical composition of herbal products by using extracts of Belamcandae Rhizoma(EBR) extracted with different polarity solvent as an example, and evaluate the quality of EBR based on the analysis of chemical profiling, efficacy evaluation and pharmacokinetics. As seen from the results of chemical profiling, the PCA and PLS-DA score plot indicated that the dots of Belamcandae Rhizoma water extracts were separated from ethanol extracts obviously, which suggested significant differences of chemical profiling existing in the different solvent extracts. The PCA and PLS-DA loading plot illustrated that the main compounds contributing to chemical profiling differences were tectoridin(TD), iristectorin B(IT B), iridin(ID), tectorigenin(TG), irigenin(IG), iristectorigein A(IG A), dichotomitin(DT) and irisflorentin(IF). Furthermore, the results of HPLC analysis demonstrated that the contents of these main compounds in ethanol extracts were significantly higher than that in water extracts (P < 0.01). Both the pharmacological and hematoxylin-eosin staining studies indicated that the ethanol extracts of Belamcandae Rhizoma had a better therapeutic effect than water extracts in oral ulcer model rats (P<0.01). It is suggested that the ethanol extracts were beneficial to the absorption and bioavailability of TG which was one of the most important bioactive compounds of Belamcandae Rhizoma in pharmacokinetic study in rats. This work provided a novel method to optimize the extraction process of EBR and related herbal products. Compared with the conventional chemical fingerprint methodology, the approach proposed above is not only a powerful tool to identify efficacy-related components for the quality evaluation, but also can be used to predict the therapeutic efficacy of herbal products.