Based on sodium cholate as chiral selector, four stereoisomers of palonosetron hydrochloride, i.e. PALO (3aS, 2S), PALO (3aR, 2R), PALO (3aS, 2R), and PALO (3aR, 2S), have been separated by five EKC modes, i.e. MEKC, solvent-modified MEKC, cosurfactant-modified MEKC, MEEKC, and MEEKC without cosurfactant. The performances of different modes were compared. The migration order and its change with experimental conditions were elucidated. In every mode studied, the migration orders in each enantiomeric pair were (3aS, 2S), (3aR, 2R) and (3aS, 2R), (3aR, 2S), respectively, determined by the selectivity of chiral selector (chromatographic mechanism). Enantiomeric pair (3aS, 2S), (3aR, 2R) was eluted before enantiomeric pair (3aS, 2R), (3aR, 2S) due to mobility difference (electrophoretic mechanism). For the separation between (3aR, 2R) and (3aS, 2R), the second enantiomer of the first pair and the first enantiomer of the second pair, two mechanisms gave opposite migration orders according to the measured selectivity and mobility data. Therefore, three different migration orders were observed at different conditions, depending on the relative strength of two effects.