The complexity of herbal matrix necessitates the development of powerful analytical strategies to enable comprehensive multicomponent characterization. In this work, targeting the multicomponents from Panax japonicus C.A. Meyer, both data dependent acquisition (DDA) and data-independent high-definition MSE (HDMSE) in the negative electrospray ionization mode were used to extend the coverage of untargeted metabolites characterization by ultra-high-performance liquid chromatography (UHPLC) coupled to a VionTM IM-QTOF (ion-mobility/quadrupole time-of-flight) high-resolution mass spectrometer. Efficient chromatographic separation was achieved by using a BEH Shield RP18 column. Optimized mass-dependent ramp collision energy of DDA enabled more balanced MS/MS fragmentation for mono- to penta-glycosidic ginsenosides. An in-house ginsenoside database containing 504 known ginsenosides and 60 reference compounds was established and incorporated into UNIFITM, by which efficient and automated peak annotation was accomplished. By streamlined data processing workflows, we could identify or tentatively characterize 178 saponins from P. japonicus, of which 75 may have not been isolated from the Panax genus. Amongst them, 168 ginsenosides were characterized based on the DDA data, while 10 ones were newly identified from the HDMSE data, which indicated their complementary role. Conclusively, the in-depth deconvolution and characterization of multicomponents from P. japonicus were achieved, and the approaches we developed can be an example for comprehensive chemical basis elucidation of traditional Chinese medicine (TCM).