In this study, the Jerusalem artichoke polyfructose was purified by the simulated mobile chromatography (SMC) and sequential simulated mobile bed (SSMB) according to the results of single column chromatographic system, which the parameters of the SMB and SSMB were investigated. Based on the results, the SSMB was the better technology and the optimized process parameters were as follows, feed concentration of 30%, ratio of material to solvent of 1.1∶1.0. Under these conditions, the concentration of the Jerusalem artichoke polyfructose was 17.9%, the purity was 96.9%, and the recovery was 95.8%, which was 17.7% higher than the material.