According to the strong application background of bioflavonoid and metal-flavonoid complexes, novel electrospray ionization tandem mass spectrometry (ESI-MS n ) was applied to investigate the structure and fragmentation mechanism of transition metal-rutin complexes. In the full-scan mass spectra, different stoichiometric ratios of rutin-metal complexes were found. In the reaction between rutin and Cu, four kinds of complexes with four different stoichiometric ratios were produced. In the reaction between rutin and Zn, Mn(II), and Fe(II), only two kind of complexes with stoichiometric ratios of 1:1 and 1:2 occured. In further tandem mass spectrometric experiments of different rutin-metal complexes, product fragments came from the neutral loss of the external rhamnose and the internal glucose unit, oligosaccharide chain, aglycone, and small organic molecules. According to the MS n data, we proposed a mechanism for all fragments of the rutin-Cu complex A and the structure of two rutin-Cu complexes, C and D.