The simulated moving bed (SMB) is potentially an economical method for the separation and purification of natural products because it is a continuous processes and can achieve higher productivity, higher product recovery, and higher purity than batch chromatographic processes. Despite the advantages of SMB, one of the challenges is to specify its zone flow rates and switching time. In this case it is possible to use the standing wave analysis. In this method, in a binary system, when certain concentration waves are confined to specific zones, high product purity and yield can be assured. Appropriate zone flow rates, zone lengths and step time are chosen to achieve standing waves. In this study the effects of selectivity on yield, throughput, solvent consumption, port switching time, and product purity for a binary system are analyzed. The results show that for a given selectivity the maximum throughput decreases with increasing yield, while solvent consumption and port switching time increase with increasing yield. To achieve the same purity and yield, a system with higher selectivity has a higher throughput and lower solvent consumption.