Chromatographic separation processes such as simulated moving bed (SMB) are widely used in the petrochemical, fine chemical, sugar, and pharmaceutical industries. Their separation efficiency can be improved by optimizing the components' adsorptivity in the different unit sections through, e.g., the use of solvent, temperature, or PH gradients. In this work, the salt gradient ion-exchange SMB used to separate two proteins, beta-lactoglobulins A and B, is theoretically analyzed, where the protein adsorption is described by the steric mass action model. Detailed model-based sequential optimization studies have been carried out for both closed-loop isocratic SMB as well as closed and open-loop gradient ion-exchange SMB. The separation efficiency is described by the throughput. Different gradient cases were analyzed to find out the influence factors. The results show that the gradient SMB is more efficient than the isocratic SMB in terms of startup time, throughput, and desorbent-to-throughput ratio. Moreover, it can be known that using open-loop gradient ion-exchange SMB to separate proteins is more effective than using closed-loop gradient SMB. The influencing factors such as the mass transfer efficiency and the maximum flow rate on separation efficiency are discussed according to different cases.