Isoliquiritigenin is one of major active component in licorice, which plays an important role in pharmaceutical fields. It was purified by a three-zone simulated moving bed (SMB) at laboratory scale in this paper. The comparison of the isoliquiritigenin separation with different column configurations was shown that the highest purity product was achieved in 1:1:2 configuration mode. It was obtained 99% in final purity of isoliquiritigenin by combing with partial collection method, which is potentially useful for the purification of target product from multi-components sample.