Flavonoids occupy the largest family of natural products and possess a broad spectrum of health benefits. Their metabolites are sometimes the truly effective molecules in vivo. It is still challenging, however, to unambiguously identify flavonoid metabolites using conventional LC-MS/MS. Herein, we aimed to pursue auxiliary structural clues to m/z values in both MS1 and MS2 spectra through LC coupled to three-dimensional MS (LC-3D MS). MS1, as the first dimension, was in charge of suggesting theoretical molecular formulas, MS2, the as second dimension, was responsible for offering substructures, and exactly, online energy-resolved MS (ER-MS), as the third dimension, provided optimal collision energies (OCEs) that reflected the linkage manners among the substructures. Metabolic characterization of a natural sweet taste modulator, namely, (R)-7,3′-dihydroxy-4′-methoxy-8-methylflavane (DHMMF), was conducted as a proof-of-concept. Extensive efforts, such as full MS1 and MS2 scans on IT-TOF-MS and predictive selected-reaction monitoring mode on Qtrap-MS, were made for in-depth metabolite mining. Seventeen metabolites (M1-M17) were captured from DHMMF-treated biological samples, including 17 (M1-M17), 10 (M4-M9, M11, M13, M14, and M16), and 2 (M5 and M10) metabolites from urine, plasma, and feces, respectively. Their structures were configured by integrating MS1, MS2, and OCE information. Except M10, all metabolites were new compounds. LC-MS/MS-guided chromatographic purification yielded three glucuronyl-conjugated metabolites (M5, M8, and M11), and NMR spectroscopic assays consolidated the structures transmitted from LC-3D MS. Demethylation, glucuronidation, and sulfation occurred as the primary metabolic pathways of DHMMF. Above all, LC-3D MS bridged LC-MS/MS from putatively structural annotation toward confidence-enhanced identification, beyond the metabolite characterization of flavonoids.