Belamcandae Rhizoma is a widely used traditional Chinese herbal medicine with isoflavones as the main active ingredient. In this paper, an integrated strategy was developed to discover and identify new isoflavones in Belamcandae Rhizoma by an ultra-high-performance liquid chromatography coupled with high resolution multistage mass spectrometry. Different characterization methods were used based on structural features of isoflavone aglycones and glycosides. On one hand, we adopted a data-dependent acquisition mode incorporated into intelligent AcquireX deep scan algorithms to analyze crude extract, and used a mass defect filtering technique to filter out two kinds of isoflavone aglycones from the extract. On the other hand, neutral-loss-triggered MSn was used to analyze isoflavone glycosides, and under this acquisition mode, MSn scan only took place when chemical components exhibited specific neutral losses. Identification of isoflavones was achieved either by comparison with reference compounds or analysis of characteristic product ions based on MS2 or MSn fragmentation patterns. UV absorbance spectra also contributed to the confirmation of isoflavones. As a result, a total of 65 isoflavone aglycones (42 new aglycones) and 142 isoflavone glycosides (122 new glycosides) were discovered, including a number of trace components. Meanwhile, modifications of new sugar moieties, such as xylose, rhamnose and 6-O-(4‑hydroxy-3,5-dimethoxybenzoyl)-β-D-glucose, were discovered in Belamcandae Rhizoma for the first time. These results indicated the feasibility of this established strategy for in-depth identification of new isoflavone aglycones and glycosides.