A new method, namely negative-pressure cavitation extraction (NPCE), followed by liquid chromatography-tandem mass spectrometry (LC-MS/MS) is presented for the extraction and quantification of flavonoids in pigeon pea leaves. This method combines the high efficiency of NPCE and the sensitivity and accuracy of MS/MS. The influential parameters of the NPCE procedure including liquid/solid ratio, extraction time, nitrogen flow and number of extraction cycles were optimized. Under optimized conditions, the efficiency of NPCE for extracting five flavonoids was compared to microwave-assisted extraction (MAE), ultrasonic extraction (USE) and heating reflux extraction (HRE). Additionally, structural disruption to pigeon pea leaves samples with different extraction methods was investigated by scanning electron microscopy. The relative recovery with NPCE was equivalent to or higher than that with USE and obviously higher than those with MAE and HRE which are usually conducted in higher temperatures. Furthermore, because NPCE was performed with nitrogen at room temperature, the degradation and oxidation of analytes were avoided. In addition, the NPCE method was validated in terms of repeatability and reproducibility, relative standard deviation for relative recovery was lower than 5.84 and 8.83%, respectively. The method was also successfully applied for the quantification of five flavonoids in pigeon pea leaves. All these results suggest that the developed NPCE-LC-MS/MS method represents an excellent alternative for the extraction and quantification of flavonoids in other plant materials.