A novel on-column labeling method of amino acid (AA) enantiomers by using dansyl chloride (Dns-Cl) has been explored combined with chiral ligand-exchange CE (CLE-CE) technique and UV detection. Efficient labeling was achieved by sequential injection of buffer, Dns-Cl, AA enantiomers, Dns-Cl and buffer at 0.2 psi for 10.0, 3.0, 24.0, 3.0, and 10.0 s, respectively. After injection, the sandwich sections were allowed to react at room temperature for 35.0 min. With this procedure, successful on-column labeling and CLE-CE separation of 17 pairs AA enantiomers have been achieved with a buffer of 100.0 mM boric acid, 5.0 mM ammonium acetate, 3.0 mM ZnSO4 and 6.0 MM L-Arg at pH 8.4, giving nine pairs fully enantioresolved with resolution in between 2.0 and 5.1. CLE-CE of some individual and mixed pairs was also demonstrated, much the same as using pre-column labeling. As validated by both artificially prepared solutions and serum samples, this new method was shown to be applicable to the quantitative analysis, with a linear range between 14.0 mu M and 3.7 mM, correlation coefficient above 0.99 and recovery in between 90.4% and 111.7%. It was also demonstrated that the migration time-temperature based curve allows for temperature determination in CE by using this new method.