A new method, Ionic liquid-based negative pressure cavitation-assisted extraction (ILs-NPCE) was investigated to extract three main flavonoids genistin, genistein and apigenin from pigeonpea roots. The influential parameters of the ILs-NPCE were optimized by the single factor and the BBD (Box-Behnken design) experiments. [C(8)mim]Br was used as the experiment ionic liquid, the optimal conditions were: temperature 74 degrees C, negative pressure -0.07 MPa, liquid/solid ratio 20:1 mL/g, concentration 0.53 M and extraction time 15 mm. The maximum extraction yields of genistin, genistein and apigenin were 0.482 +/- 0.008, 0.496 +/- 0.017 and 0.291 +/- 0.015 mg/g, respectively. The extraction kinetics were also studied under the optimized conditions and it indicated that the ILs-NPCE showed much more advantages such as higher extraction yields, shorter time and more environmental friendly process than other methods. Moreover, this extraction method was also applied with pilot-scale extraction and their yields were 0.477 +/- 0.013, 0.480 +/- 0.014 and 0.271 +/- 0.021 mg/g, respectively. Thus, it was indicated that the developed ILs-NPCE method could be an alternative method for natural compounds extraction in industry. (C) 2013 Elsevier B.V. All rights reserved.