The structural annotation of metabolites now relies heavily on HR-MS/MS information, resulting in ambiguous identities in most cases. More auxiliary evidence is therefore desired to achieve confirmative identification. Herein, we made an attempt to involve retention time (t) along with optimal collision energy (OCE) as the additionally structural clues, and the applicability validation was conducted via confidence-enhanced metabolite characterization of echinacoside, an antidementia drug candidate within clinical trials. Quantitative structure-retention relationships (QSRR) were modeled via assaying 184 authentic compounds on RPLC, HILIC, and serially coupled RPLC and HILIC (RPLC-HILIC). Online energy-resolved MS was developed to yield breakdown graphs for selected ion transitions, and OCE was demonstrated to be superior to CE toward pointedly denoting the bonds-of-interest. Nineteen metabolites (M1-M19) were confidently identified in biological samples from echinacoside-treated rats by analyzing m/z values first to yield empirical formulas and substructures, and t and OCE subsequently contributed to sift the candidate structures. Structural identification was validated by oral administration of three relevant compounds in parallel and chromatographic purification as well. Above all, the integration of retention and dissociation behaviors enabled promoting one step forward for structural annotation confidences merely relied on HR-MS/MS.