Natural products are considered as potential sources of leading compounds and play an important role in drug discovery. The liquid chromatography-mass spectrometry (LC-MS) technique is a powerful tool for compound-guided isolation from natural products. In this study, a high-efficiency integrated strategy was adopted to improve the new leading compounds discovery, including offline two-dimensional (2D) LC to extend the peak capacities, target neutral loss (NL) data-dependent acquisition (DDA) for barrigenol-type triterpenoids saponins and automatic screening through predicted natural product screening (PNPS) in TraceFinder. To validate the integrated strategy, the shell of Xanthoceras sorbifolium Bunge (XSB) was taken as a case. An offline 2D-LC system was constructed with hydrophilic interaction chromatography (HILIC) and reversed phase (RP) C18 column, and orthogonality of 0.66 and peak capacity of 3494. The 2D-LC system improved chromatographic baseline separation and peak resolution. Full MS/all ion fragmentation (AIF)/NL dd-MS2 DDA was employed for the detection of the barrigenol saponins. PNPS strategy was adopted and markedly extended the screening coverage. The combined strategy showed about 5 times improvement in the screening capability. The PNPS screening process, using TraceFinder software, discovered a total of 752 barrigenol saponins from the shell of XSB, including 707 potentially new barrigenol saponins, accounting for 94.02%. The feasibility of the strategy was also confirmed by the isolation of two novel barrigenol saponins, the structures of which were unambiguously identified using nuclear magnetic resonance (NMR). Furthermore, this strategy could also be applied to rapidly discover new bioactive constituents from other herbal medicines or other natural sources, especially the barrigenol saponins constituents.