IT-MS operated in the positive mode was applied for the rapid characterization/quantification of the flavanones in extracts from Fructus aurantii. APCI-MS and CID MS/MS provide unequivocal molecular weight (MW) data of these compounds and useful information about their structures (diagnostic fragment ions). Main fragment pathways include neutral losses of H2O, C2H2O, and B-ring as well as a retro-Diels-Alder (RDA) fragment giving rise to [1,3A + H], [1,3B+H]+, and [1,4B-H2 + H]+ ions, which form the characteristic MS/MS "fingerprint" of flavanone aglycones. When screening extracts of F. aurantii for flavanone aglycones, eight target compounds were characterized using this fingerprint. Meanwhile, ESI-MS in full-scan mode was developed and validated for the quantification of the main flavanone aglycones in F. aurantii. This method is simple, accurate, fast and requires only 16 min per sample for direct detection and quantification of naringenin and hesperetin. All the results and these characteristic fragments showed that the IT-MS is a powerful tool for the structural characterization and quantitative determination offlavanone aglycones.