In this study, a liquid chromatography/diode array detector-atmospheric pressure chemical ionization/mass spectrometry (LC/DAD-APCI/MS) was successfully developed to identify and characterize the main flavonoids and caffeoylquinic acids (CQAs) of three common Compositae plants (Chrysanthemum morifolium Raman, Artemisia annua, and Chrysanthemum coronarium) which have been used as herbal medicine. Identifications were performed by comparing the retention time, UV and mass spectra of samples with standards or/and earlier publications. The crude methanolic extracts of these plants were assayed directly using LC/MS without any further pretreatment. The proposed method is rapid and reproducible and is useful for characterization and evaluation of different plant flavonoids and CQAs. A total of 41 different flavonoids and 6 CQAs were identified and confirmed by APCI-MS. The main components of three Compositae plants were also compared. Although there exist some similarities in the flavonoidic content of the leaf and flower of C. morifolium, significant variations in their varieties and concentrations were observed. Artemisia annua processes substantial amount of alkylated derivatives of flavones and Chrysanthemum coronarium contains only CQAs. These findings suggest that although all the plants studied are from the same Compositae family, their flavonoids and phenolic compositions are markedly different. The proposed method is useful for further chromatographic fingerprinting of plant flavonoids.