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The co-elution, pervasive isomers, and frequently occurring in-source fragmentation definitely hinder the comprehensive characterization of the multiple components from traditional Chinese medicine (TCM) by liquid chromatography/mass spectrometry. Herein, a dimension-enhanced strategy, by utilizing an ion mobility quadrupole time-of-flight mass spectrometer coupled to ultra-high performance liquid chromatography (UHPLC/IM-QTOF-MS) with the ability of offering four-dimensional information (retention time, Rt; drift time or collision cross section, CCS; accurate mass of precursors; and accurate MS2 product ions), is presented. Shuanghe Decoction (SHD) is a classic tonifying formula composed of nine herbs, however, little is known to its chemical complexity, hitherto. Good chromatographic separation was achieved on an HSS T3 column, and by the Vion™ IMS-QTOF high-resolution mass spectrometer, data-independent MSE and High-Definition MSE (HDMSE) in both the negative and positive electrospray ionization modes were employed for acquiring the collision-induced dissociation-MS2 data. A self-built database, including 642 known compounds, was established, which assisted to perform the automated peak annotation by UNIFI™. By reference to 55 compounds, totally 236 components were identified or tentatively characterized from SHD with 4D data recorded. The combination of negative and positive modes could yield more information complementary to structural elucidation. Compared with the conventional MSE, HDMSE exhibit of merits in the provision of CCS, better separation and detection those easily co-eluting components, and reduction of the false positives in the identification results. Conclusively, the combination of HDMSE acquisition, in-house library, and UNIFI-facilitated automated peak annotation, renders a potent approach dedicated to deconvoluting the chemical composition of complex systems like TCM formulae.