Much Literature is available with respect to the collision-induced dissociation (CID) of different subtypes of flavonoid aglycones. However, a simultaneous comparison study of the common flavonoid subtypes under unified conditions is rarely reported, which is of crucial significance for their rapid structural elucidation. This study depicted the negative CID of 40 free flavonoids (comprising nine different subtypes) utilizing electrospray ionization ion-trap tandem mass spectrometry (ESI-IT-MSn). High-accuracy quadrupole time-of-flight mass spectrometry was employed to confirm the chemical formula of proposed key fragments. Specific fragmentation features were discovered among different flavonoid subtypes in terms of the essential collision energy, base peak, RDA fragmentation, and diversity of fragmentation pathways: CID of flavanones, chalcones and flavanonols was in need of lower Levels of collision energy [<40%) and exhibited simplified fragmentation pathways; overriding neutral loss of CO2 was detected for flavones, aurones and xanthones, while isoflavones preferred neutral loss of CO; 1,2A- and 1,3A- fragments were respectively dominant for flavonols and flavanones/chalcones, white homoisoflavones underwent specific radical elimination of ring B or methylene-ring B. These differentiated fragmentation characteristics integrating UV absorption resulted in the establishment of a decision tree to characterize and distinguish the common flavonoid subtypes. This study firstly revealed remarkable differentiations in the negative CID behavior of nine common flavonoid aglycone subtypes and the proposed determination strategy would much benefit the screening and rapid characterization of flavonoids from complicated matrixes by tandem mass spectrometry.