The fragmentation behaviors of quercetin and morin were analyzed and compared by the quantum chemistry method with electrospray ionization mass spectrometry（ESI-MS） in negative ion mode.Based on the density functional theory（DFT），at the level of B3LYP/6-31G（d），quantum chemistry calculation was carried out to optimize the molecular spatial configurations of quercetin and morin，in order to confirm the stable geometric configurations and deprotonation locations of quasi-molecular ions.The energy of fragment ions on the stable state under the relative framentation voltage in the second order mass spectrometry，was calculated at the level of RB3LYP/6-31+G（2d,2p）.The fragmentation pathway was deduced by comparing the stable configurations of quasi-molecular ions and combined with basis set superposition error（BSSE）-corrected bond dissociation energy（BDE）.The results indicated that the stable configuration of quercetin was that the A，B，C rings stayed in the same plane，but morin was not like this because of the 2′-OH，and the dihedral angle between B ring and AC rings was-134.662 4°.The fragmentation processes of quercetin and morin occurred mainly through the cross-ring cleavages of C ring with various of cleavage ways.The precedence order was：1,2 cleavage，0,2 cleavage，1,3 cleavage，1,4 cleavage and 0,4 cleavage，the fragment ions of 1,2A-，0,2A-，1,3A-，1,4A- and 0,4A- were generated，respectively.The difference between them was that the existence of 2′-OH on morin facilitated the cross ring cleavages.Subsequently，the rest of fragment ions were produced step by step.This study provided a theoretical basis for further revealing the fragmentation pathway of flavonol compounds.