Danggui Buxue decoction (DBD), a classic prescription of traditional Chinese medicine (TCM) for invigorating qi and generating blood, contains honey-processed Astragali Radix (HAR) and wine-processed Angelicae Sinensis Radix (WDG) in its original prescription. In this study, the compositions of DBD, WDG, and HAR were characterized using ultra-high-performance liquid chromatography coupled with the quadrupole-time-of-flight tandem mass spectrometry technique in combination with molecular network and diagnostic ion strategies. Finally, 200 compounds were identified in DBD, 114 compounds were identified in WDG, and 180 compounds were identified in HAR; there were 48 common compounds in total. The results demonstrated that compatibility led to changes in the chemical composition of TCM, and the qualitative method used in this study provided an effective data processing strategy for the characterization of components and the database for the study of the compounding mechanism of TCM.