Profiling flavonoids in natural products poses a great challenge due to the diversity of flavonoids, the lack of commercially available standards, and the complexity of plant matrixes. The increasingly popular use of ultra-high-performance liquid chromatography-diode array detection-high resolution accurate mass-mass spectrometry (UHPLC-HRAM-MS) for the analysis of flavonoids has provided more definitive information but also vastly increased amounts of data. Thus, mining of the UHPLC-HRAM-MS data is a very daunting, labor-intensive, and expertise-dependent process. An automated data processing tool, FlavonQ, was developed that can transfer field-acquired expertise into data analysis and facilitate flavonoid research. FlavonQ is an "expert system" designed for automated data analysis of flavone and flavonol glycosides, two important subclasses of flavonoids. FlavonQ is capable of data format conversion, peak detection, flavone and flavonol glycoside peak extraction, flavone and flavonol glycoside identification, and production of quantitative results. An expert system was applied to the determination of flavone and flavonol glycosides in nine different plants with an average execution time of less than 1 min. The results obtained by FlavonQ were in good agreement with those determined conventionally by a flavonoid expert.