Eight types of ionic liquid (IL) were synthesized in this paper, and ionic liquids-based microwave-assisted extraction (ILs-MAE) technique was used to extract quercetin from the Chinese herbal medicine Toona sinensis. Several significant operating parameters were optimized by a series of single factor experiments and orthogonal design L9 (34) experiments in this work. Compared with liquid-based maceration extraction (ILs-ME), liquid-based heat extraction (ILs-HE) and liquids-based ultrasound-assisted extraction (ILs-UAE), the optimized approach of ILs-MAE technique cost the shortest time but afforded the highest extraction amount. Moreover, reversed phase high performance liquid chromatography (RP-HPLC) with ultraviolet detection (UV-DAD) was employed for the analysis. The results show that the amount of quercetin extracted by [Bmim]Br was 182.78 mg g−1 with RSD 1.02%. The developed approach is linear between concentrations from 15.20 mg L−1 to 213.2 mg L−1 of quercetin and the regression coefficient (R) was 0.9992. The recoveries of quercetin extracted by these four methods were 95.07%–105.8% with RSDs lower than 3%. Furthermore, the change of the microstructure and chemical structure of the sample before and after different extraction procedures were researched, respectively. Because of the remarkable dissolving capacity of ILs aqueous solution and the obvious destruction on sample surface microstructures during ILs-MAE process, ILs-MAE technique got the highest extracted amount. With the help of LC-MS, we can further confirm that Toona sinensis do contain the active ingredient of quercetin and ILs had no interference of quercetin.
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