In traditional Chinese medicine, Lysimachiae Herba (LH) and Desmodii Styracifolii Herba (DSH) have been widely used for the treatment of calculi, but there is a certain focus in clinical application. Flavonoids as their pharmacologically active substances were focusly studied to make clear of their chemical compositions and reveal the similarities and differences between LH and DHS by analysis of characteristic marker components at the molecular level. An ultra high performance liquid chromatography quadrupole time of-flight tandem mass spectrometry (UPLC-QTOF-MS/MS) approach based on metabolite profiling was established. The high-resolution data was acquired through data dependent acquisition (DDA) mode. Based on the targeted and untargeted analytical strategies, a total of 113 compounds were identified, of which 80 compounds existed in LH and 61 in DSH. Then multivariate statistical analysis was applied to further find the characteristic marker components, and a total number of 21 variables were screened as the valuable variables for discrimination. By matching with identified flavonoids, these 21 variables were corresponding to 15 flavonoids (including 6 from LH and 9 from DSH) which were firstly identified as the marker compounds. These results indicated that the UPLC-QTOF-MS/MS method with analysis strategy was a powerful tool for rapidly identification and screening of marker compounds of flavonoids between LH and DSH, and the 15 screened marker compounds provide a chemical basis for the further researches on the mechanisms of LH and DSH in the treatment of cholelithiasis and nephrolithiasis respectively. (C) 2019 Elsevier B.V. All rights reserved.