Abstract: A coated capillary with 3-aminopropyltriethoxysilane modified magnetic nanoparticles(APTES-MNPs)as the stationary phase was constructed and applied in enantio-separation in capillary electrophoresis. The magnetic nanoparticles coating inside the capillary columns could be easily generated by applying and removing the external magnetic field. The APTES-MNPs-coated capillary showed long lifetime, superior chemical stability and good reproducibility. It endured during more than 80 replicated analyses and was tolerant to HCl(0. 01 mol/L), NaOH(0. 001 mol/L), CH₃OH and CH₃CN. The APTES-MNPs-coated capillary can be applied to enantioseparation of basic drugs. Compared with the uncoated capillary system, improved separation of the tested enantiomers(ofloxacin and propranolol)were obtained in the system based on APTES-MNPs-coated capillary. Several primary parameters such as chiral selector concentration, running buffer pH, organic solvent and applied voltage, were systematically optimized in order to obtain successful chiral separation. The results indicate that the application of magnetic nanoparticles is a promising way in chiral separation.