Metabolite identification for the compounds that undergo multiple and sequential metabolism is still a great challenge. Echinacoside (ECH), a typical phenylethanoid glycoside, contains multiple unstable chemical bonds and high reactive functional groups which are susceptible to multiple pathways of degradation and metabolism, leading great difficulties for its metabolite identification. This study proposed a novel approach for rapidly identifying the complicated and unpredictable metabolites of ECH, based on the powerful liquid chromatography hybrid ion trap and time of flight mass spectrometry (LC/MS-IT-TOF) analysis. Four degradation products were rapidly identified via the "fragmentation-degradation" comparisons. Five phase I and phase II metabolites of the degradation products were rapidly characterized via the crossover mass differences comparisons of their quasi-molecular ions with the potential precursors. Four direct phase I and phase II metabolites of the parent compound were identified by the mass differences analysis of the molecular ions between metabolites and the parent compound. Multiple stages of fragmentation patterns were used to confirm the metabolites characterizations. This study provides a novel approach to characterizing the complicated metabolites, and would be widely applicable for the metabolite identification of natural products.