Chiral separation of 12 pairs of basic analyte enantiomers including oxybutynin, bambuterol, tradinterol, clenbuterol, clorprenaline, terbutaline, tulobuterol, citalopram, phencynonate, fexofenadine, salbutamol, and penehyclidine was conducted by capillary electrophoresis using a single-isomer anionic β-cyclodextrin derivative, heptakis-(2,3-diacetyl-6-sulfato)-β-cyclodextrin as the chiral selector. Parameters influencing separation were studied, including background electrolyte pH, heptakis-(2,3-diacetyl-6-sulfato)-β-cyclodextrin concentration, buffer concentration, and separation voltage. A background electrolyte consisting of 50 mM Tris-H3 PO4 and 6 mM heptakis-(2,3-diacetyl-6-sulfato)-β-cyclodextrin at pH 2.5 was found to be highly efficient for the separation of most enantiomers, with other conditions of normal polarity mode at 10 kV, detection wavelength of 210 nm using hydrodynamic injection for 3 s. Under the optimal conditions, baseline resolution (>1.50) for 11 pairs of enantiomers and somewhat lower resolution for penehyclidine enantiomers (1.17) were generated. Moreover, the possible mechanism of separation of clenbuterol, oxybutynin, salbutamol, and penehyclidine was investigated using a computational modeling method.