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As a holoparasitic plant, Cistanche deserticola is one of the two original sources of Cistanches Herba that is one of the most famous tonic medicines, in Chinese Pharmacopoeia. The succulent stems are used for medicinal usage, whereas those lignified stems as well as flowers of less pharmacological importance are usually deserted, suggesting extensive resource waste. Herein, chemical characterization of the flowers along with lignified stems was conducted using HPLC-IT-TOF-MS aiming to explore the medicinal valu of those non-medicinal parts. Following ultrasonication-assisted extraction with 50% aqueous methanol, either flower or lignified stem extract was subjected onto LC-IT-TOF-MS equipped with a Capcell core ADME column to acquire both MS¹ and MSº spectra, and gradient elution was carried out with combinatory 0.1% aqueous formic acid and acetonitrile. Both positive and negative ionization polarities were deployed, resulting in the observation of 62 components, in total. Thirty-nine signals were structurally annotated, including phenylethanoid glycosides, iridoids, lignans and saccharides according to matching with authentic components and literature information, as well as applying the proposed mass fragmentation rules. A total of 62 ones were putatively identified. Above all, lignified stems and flowers should not the qualified substitutes for the succulent stems attributing to the significant differences between the medicinal portion and those parts with less medicinal values.