Separation of an amino acid mixture using continuous rotating annular ion-exchange chromatography is numerically simulated by a newly constructed mathematical model. Dissociation reactions of amino acids and eluent buffer components, Nernst-Planck-type intraparticle ionic transport, and a nonlinear ion-exchange equilibrium based on ion-exchange selectivity are considered in the model. The simulated and the experimental results agree well under various operation conditions. The effects of rotation speed of the annular bed and the interstitial liquid velocity on separation are studied experimentally and theoretically.