The novel desalination device, the return flow electromembrane desalination called Return Flow Ion-Concentration-Polarization (RF-ICP) which resolved one of the most prominent problems in ICP is the over-limiting conduction mechanism. The development of the ion depletion layer largely determines the energy consumption of electromembrane desalination, because of the increased electrical resistance of the ion-depleted boundary layer which is also a desired outcome for desalination. In this work, we conducted a study on the desalination efficiency of the RF-ICP desalination system for different operations. The transport of ions in the system was examined by using numerical simulation. The Poisson-Nernst-Planck and Navier-Stokes equations were solved numerically to model the transport of ions at different electrical current regimes and the feeding-flow rates. Obtained simulation results showed that the current and current efficiency increases with the feeding-flow rate, the salt removal ratio changes inversely with feeding-flow rate, and the energy per ion remove decreases when increasing the feeding-flow rate. The findings are useful in optimizing the design and operation of the RF-ICP desalination system.