An effective method was developed for screening licorice roots and fritillary bulbs for contamination by aflatoxin B(1) and ochratoxin A using high-performance liquid chromatography connected to tandem mass spectrometry (HPLC-MS/MS). The samples were pre-concentrated and purified using solid-phase extraction, which provided satisfactory results. The separation was performed on a Waters Xbridge(TM) C18 column with a linear gradient of acetonitrile - water containing 5mM ammonium acetate. The MS spectrum was acquired in positive mode with both single quadrupole (Q1) and multiple reaction monitoring (MRM). The optimised method offered a good linear correlation (r(2)>0.9967), excellent precision (RSD<2.83%) and acceptable recovery (from 92.78 to 105.37%). The limits of detection (LOD) and the limits of quantification (LOQ) were less than 0.024 μg/kg and 0.095 μg/kg, respectively. The validated method was successfully applied to the rapid screening for AFB(1) and OTA in licorice roots and fritillary bulbs.