C-Glycosyl quinochalcones are unique components in Carthamus tinctorius L. The reported C-glycosyl quinochalcones have the same quinochalcone skeleton with a hydroxyl group at the 5'-position and a glucose linked to this position with a carbon-carbon bond. In this study, the standard hydroxysafflor yellow A and water-extracted fraction of Carthamus tinctorius L. were analyzed by ultraperformance liquid chromatography coupled with quadrupole-time-of-flight mass spectrometry (UPLC/Q-TOFMS) in both positive and negative ion modes. The fragmentation pathways of C-glycosyl quinochalcones were interpreted and validated by accurate mass measurement. Their fragmentation showed a special cleavage at the C-C bond except for the typical internal cleavage at the sugar moiety of other C-glycosyl flavonoids. In positive ion mode, cleavage of the 5'-glucose produced an [M+H-162](+) ion by a neutral loss, while cleavage of the 5'-glucose in negative ion mode led to an [M-H-163](-.) ion by radical cleavage. The cleavage from the carbonyl group produced fragment ions containing an A or a B ring. The fragment ions containing an A ring were common product ions of seven compounds in both ion modes, and fragment ions containing the B ring were used to judge the different substituent groups at the 3'-position. The fragmentation patterns of seven structurally related C-glycosyl quinochalcones were analyzed systematically and the formation of the fragment ions in two modes is explained in detail in this report. UPLC/Q-TOFMS is an effective tool for characterizing a complex sample, which gives higher resolution separation and generates accurate mass measurement of the product ions.