The effect of the electric field and surface morphology of corrugated graphene (GE) layers on their capacitive deionization process is studied using molecular dynamics simulations. Deionization performances are evaluated in terms of water flow rate and ion adsorption and explained by analysing the water density distribution, radial distribution function and distribution of the ions inside the GE layers. The simulation results reveal that corrugation of GE layers reduces the water flow rate but largely enhances ion adsorption in comparison to the flat GE layers. Such enhancement is mainly due to the adsorption of ions on the GE layers due to the anchoring effect in the regions with wide interlayer distances. Moreover, it reveals that the entrance configuration of the GE layers also has a significant effect on the performance of deionization. Overall, the results from this study will be helpful in designing effective electrode configurations for capacitive deionization.