A rapid, accurate and precise method for the determination of 22 amino acids in Isatidis Radix by Hydrophilic Interaction Ultra-High-Performance Liquid Chromatography Coupled with Triple-Quadrupole Mass Spectrometry (HILIC-UPLC-MS/MS) was established. Chromatographic separation was carried out on a Acquity UPLC BEH Amide column ($2.1mm{ imes}100mm$, $1.7{mu}m$) with gradient elution of acetonitrile (containing 0.05% formic acid and 2 mM ammonium formate) and water (containing 0.15% formic acid and 10 mM ammonium formate) at a flow rate of 0.4 mL/min; Waters Xevo$^{TM}$ TQ worked in multiple reaction monitoring mode. All components were separated in 17 min. All calibration curves were linear ($R^2$ > 0.991) over the tested ranges. The limits of detection (LOD) and limits of quantitation (LOQ) for these compounds were 0.21-79.55 and 0.72-294.23 ng/mL, respectively. The average recoveries were in the range of 93.75-104.16% with RSD value less than 6.56%. Therefore, this method could be an alternative assay for the determination of 22 amino acids in Isatidis Radix due to its rapidness, sensitivity, less sample and solvent consumption.