To develop analytical methods for the identification and determination of the flavonoids in Sophora tonkinensis for comprehensive quality evaluation. An HPLC-DAD-ESI-MS method was used for the separation and characterization of the flavonoids in S. tonkinensis, and a liquid chromatographic method was employed to simultaneously determine five major active flavonoids in this crude drug. Seventeen flavonoids were identified, among which, seven were unambiguously identified as trifolirhizin, quercetin, formononetin, macckiain, kurarinone, sophoranone, and sophoranochromene by comparing their retention times, and UV and MS spectra with those of the authentic compounds, and the other ten flavonoids were tentatively identified by comparing their UV and MS/MS spectra with those of literature data. Furthermore, five major active flavonoids, including trifolirhizin, quercetin, maackiain, sophoranone, and sophoranochromene were determined in S. tonkinensis. All calibration curves expressed good linearity (r > 0.999 8) within the test ranges, and the recovery from this method was 96.40%-104.43%. The developed HPLC method was successfully applied to quantitatively determine the five flavonoids in seventeen samples of S. tonkinensis. The developed method rapidly characterized the bioactive flavonoids of S. tonkinensis, and could be readily utilized to enhance the quality assurance approaches for this traditional Chinese medicine.