Amino acid ionic liquids (AAILs) with l-lysine (l-Lys) as anion were synthesized and applied as new chiral ligands in Zn(II) complexes for chiral ligand-exchange CE. After effective optimization, baseline enantioseparation of seven pairs of dansylated amino acids was achieved with a buffer of 100.0 mM boric acid, 5.0 mM ammonium acetate, 3.0 mM ZnSO4, and 6.0 mM [C6mim][l-Lys] at pH 8.2. To validate the unique behavior of AAILs, a comparative study between the performance of Zn(II)-l-Lys and Zn(II)-[C6mim][l-Lys] systems was conducted. In Zn(II)-[C6mim][l-Lys] system, it has been found that the improved chiral resolution could be obtained and the migration times of the three test samples were markedly prolonged. Then the separation mechanism was further discussed. The role of [C6mim][l-Lys] indicated clearly that the synthesized AAILs could be used as chiral ligands and would have potential utilization in separation science in future.