Shixiao San is a famous Traditional Chinese Medicine (TCM) formula that has been used for a long time for the treatment of gynecological diseases. In this paper, the active constituents in Shixiao San were characterized by using bioactivity evaluation followed by UPLC-QTOF and Markerlynx analysis. The analgesic activities of two extracts of Shixiao San were evaluated using the hot-plate test, acetic acid-induced writhing and dysmenorrhea mice model. The results showed that the analgesic activity of Shixiao San vinegary extract (boiling vinegar) was superior to the aqueous extract. UPLC-QTOF and Markerlynx analytic results showed that the process of boiling in vinegar may improve the dissolution of Shixiao San flavanoids, and these flavanoids may contribute to the observed analgesic activity. This work demonstrated that UPLC/QTOFMS and Markerlynx could serve as new methods for fast generation and automated analysis of information-rich data from Chinese herbal medicines.