A microwave-assisted extraction (MAE) and ultra high performance liquid chromatography coupled with diode array detection and time-of-flight mass spectrometry (UHPLC-DAD-TOF-MS) method was developed for simultaneous determination of 14 phenolic compounds in the root of Pueraria lobata (Wild.) Ohwi and Pueraria thomsonii Benth. Operational conditions of MAE were optimized by central composite design (CCD). The optimized result was 65% ethanol as extraction solvent, 17 mL of extraction volume, 100 °C of extraction temperature and 2 min of hold time. A Zorbax SB C (50 mm × 4.6 mm I.D., 1.8 μm) and gradient elution were used during the analysis. The chromatographic peaks of 14 investigated compounds in samples were successfully identified by comparing their retention time, UV spectra and TOF mass data with the reference substances. All calibration curves showed good linearity (r > 0.9997) within the test ranges. The intra-day and inter-day variations were less than 1.77% and 2.88%, respectively. The developed method was successfully applied to determine the investigated compounds in 10 samples of Radix Puerariae Lobatae and Radix Puerariae Thomsonii, respectively. The result indicated that MAE and UHPLC-DAD-TOF-MS system might provide a rapid method for the quality control of Radix Puerariae.