A novel rapid chromatographic method based on utilization of UPLC column was developed for the analysis of eight active compounds in silymarin. The analysis was performed on a Waters Acquity UPLC system with an Acquity UPLC BEH C18 column (5mm×2.1mm I.D., 1.7μm) and a gradient elution of methanol and water containing 0.01% formic acid with a run time of 9min, in which the retention time of the last analyte was 5.8min. And all eight active compounds achieved complete separation. Comparison of system performance with conventional HPLC was made with respect to analysis time, efficiency and sensitivity. The results indicated that the type of column, the type of mobile phase and the modified addition were significant to the separation of isomeric compounds in herb extracts.