A capillary electrophoresis (CE) method for the separation of four kinds of enantiomers of non-natural carboxylic amino acid was built while hydroxypropyl-β-cyclodextrin (HP-β-CD) derivations as chiral selective material. Several different β-CD derivatives were tested for the chiral separation of non-natural carboxylic amino acid, and it was proved that HP-β-CD could show better chiral selectivity. The separation of enantiomers of amino acid was obtained by CE in a 50-μm i.d.×60 cm (effective length 45 cm) fused-silica capillary at 18 kV voltage, while 10 mM phosphate acted as running buffer and HP-β-CD served as selective material. The detective wavelength was set at 254 nm.