The chiral separations of four pharmaceutical racemates which contain N-alkyl groups were satisfactorily resolved using SBE-β-CD as a chiral mobile phase additive (CMPA) in a RP-HPLC system (the resolution is 2.701 for ondansetron hydrochloride, 1.996 for sulpiride, 1.293 for clenbuterol hydrochloride and 0.816 for omeprazole). In addition, the effects of different parameters such as CD type and CD concentration were investigated. The separation mechanism arises through the combination of several potential interactions, including electrostatic interactions as well as hydrogen bonding interactions and hydrophobic inclusion interactions, which allow for the SBE-β-CD–drug complexation with strong stereoselectivity and stability. The resolution also relates to the number and location of N atoms in the enantiomers. This method will be applicable to the isolation of various types of biologically important enantiomers containing N-alkyl groups.