Duhaldea nervosa (Wallich ex Candolle) A. Anderberg (D. nervosa) has been traditionally used as a food spice and also in folk medicine for treating traumatic injury and relieving rheumatism, especially, accelerating the healing of a fracture. However, so far as we are aware, the chemical constituents have not been fully investigated. In this study, a practical method of mass spectral trees similarity filter, a data-mining technique, was developed and evaluated for the rapid detection and identification complicated constituents based on UHPLC-LTQ-Orbitrap-MS. Finally, a total of 47 chlorogenic acids, including 19 monoacyl-quinic acids, 22 diacyl-quinic acids and 6 triacyl-quinic acids, were unambiguously or tentatively identified based on their accurate mass measurement, chromatographic retention, MSn spectra, and bibliography data. To our best knowledge, it is the first time to report the chlorogenic acids of D. nervosa, which would be benefit for the further material basis and quality research. Meantime, this mass spectral trees similarity filter method could be envisioned to exhibit a wide application for the identification of complicated components from botanical extracts. This article is protected by copyright. All rights reserved.