A new kind of chiral zirconium based metal–organic framework, l-Cys-PCN-222, was synthesized using l-cysteine (l-Cys) as a chiral modifier by a solvent-assisted ligand incorporation approach and utilized as the chiral stationary phase in the capillary electrochromatography system. l-Cys-PCN-222 was characterized by X-ray diffraction, thermogravimetric analysis, X-ray photoelectron spectroscopy, Fourier-transform infrared spectra, nitrogen adsorption/desorption, circular dichroism spectrum, zeta-potential and so on. The results revealed that l-Cys-PCN-222 had the advantages of good crystallinity, high specific surface area (1818 m2 g−1), thermal stability and chiral recognition performance. Meanwhile, the l-Cys-PCN-222-bonded open-tubular column was prepared using l-Cys-PCN-222 particles as the solid phase by ‘thiol–ene’ click chemistry reaction and characterized by scanning electron microscopy, which proved the successful bonding of l-Cys-PCN-222 to the column inner wall. Finally, the stability, reproducibility and chiral separation performance of the l-Cys-PCN-222-bonded OT column were measured. Relative standard deviations (RSD) of the column efficiencies for run-to-run, day-to-day, column-to-column and runs were 1.39–6.62%, and did not obviously change after 200 runs. The enantiomeric separation of 17 kinds of chiral compounds including acidic, neutral and basic amino acids, imidazolinone and aryloxyphenoxypropionic pesticides, and fluoroquinolones were achieved in the l-Cys-PCN-222-bonded OT column. These results demonstrated that the chiral separation system of the chiral metal–organic frameworks (CMOFs) coupled with capillary electrochromatography has good application prospects.