Cyclopamine, an inhibitor of the Hedgehog (Hh) signaling pathway, has been paid much attention in treating a wide variety of tumors. However, isolation and purification of cyclopamine analogs from medicinal plants remain challengeable. We herein proposed an efficient strategy using liquid chromatography quadrupole-time-of-flight mass spectrometry (LC-Q-TOF-MS) and liquid chromatography triple-quadrupole mass spectrometry (LC-QqQ-MS) for rapid screening and targeted isolation of cyclopamine analogs in Fritillaria and Veratrum plants. Firstly, fifteen reference compounds were characterized by LC-Q-TOF-MS and their characteristic fragment ions were summarized. Secondly, according to the characteristic fragment ions at m/z 67.1, 84.1, 109.1 and 114.1, rapid chemical screening of plant extracts was carried out by LC-QqQ-MS using precursor ion scan mode and 69 pre-target compounds were screened out. Thirdly, 24 real target compounds were verified by LC-Q-TOF-MS based on relative abundances (over 20%) of characteristic fragment ions. Fourthly, the targeted isolation of Fritillaria ussuriensis bulb and Veratrum dahuricum rhizome afforded a novel cyclopamine analog namely 15β-hydroxy-23-isopengbeisine B as well as four known ones, whose structures were determined by nuclear magnetic resonance (NMR) analysis. Additionally, these five analogs were evaluated for the inhibitory activity of Hh signaling pathway in NIH/3T3 cell and cytotoxicity in PANC-1 and HepG2 cells. These results indicated that the proposed strategy was reliable for rapid discovery and targeted isolation of important natural products from chemically complex plant matrices. © 2017 Elsevier B.V.