ABSTRACTGlucosinolates, a crucial group of secondary metabolites in Brassica vegetables, present significant chromatographic separation challenges due to their anionic form, structure diversities, and co‐existence of other phenolic compounds. This study comparatively investigated the retention and separation of seven glucosinolates using a mixed‐mode reversed‐phase/weak anion‐exchange column and a conventional reversed‐phase C18 column. Separation factors for each glucosinolate with its adjacent peaks were over 1.0 on the mixed‐mode column, while co‐eluting was observed on the C18 column. The effects of mobile phase additives and pH on the separation and retention of glucosinolates were also investigated. Results showed that glucosinolate retention was inversely related to both buffer concentration and pH. The optimized method for the mix‐mode column was applied to the complex Brassica vegetable samples. In addition to the 17 well‐resolved glucosinolate peaks, 34 peaks for phenolic compounds were identified in broccoli microgreen, suggesting the successful application scenarios for qualitative analysis in comparison with the single mode reverse phase C18 column. This study demonstrates that the mixed‐mode reversed‐phase/weak anion‐exchange column can be used as a promising separation tool for organic anions in a complex sample matrix.