Sanhua Decoction (SHD) is a classic prescription for the treatment of stroke in the clinic. Based on the combination strategy in vitro and in vivo, the chemical constituents of SHD were characterized by ultra‐high‐performance liquid chromatography coupled with quadrupole time‐of‐flight tandem mass spectrometry, and the metabolites of five effective anthraquinone aglycones (emodin, chrysophanol, rhein, aloe‐emodin, and physcion) of rhubarb in SHD were studied. A total of 222 compounds were isolated and identified in vitro, including 50 flavonoids and their glycosides, 41 coumarins, 22 anthraquinones, 22 tannins, 14 phenylpropanoids, 16 alkaloids, 18 organic acids and their esters, 14 lignans, six anthrones, and 19 other compounds. A total of 111 prototype components were isolated and identified in vivo. Among them, 26, 82, 101, and 46 prototype components and 87 metabolites were detected in plasma, urine, feces, and bile for the first time. This study provides a basis for the identification of chemical components in vivo and in vitro and the analysis of potential pharmacodynamic components of SHD, and provides a basis for further study of pharmacodynamic mechanism.