Molecular dynamics (MD) simulations are conducted to assess the Li recovery performance of three zeolitic imidazolate frameworks (ZIFs) employed as selective layers in cation exchange membranes (CEMs) for flow capacitive deionization (FCDI). The three ZIFs (ZIF-8, ZIF-8-Cl, and ZIF-8-Br) share a common metal node (Zn node) but differ in their functional groups on the imidazolate linkers (CH 3 , Cl, and Br). The performance of the ZIFs is evaluated based on their Li + /Na + selectivity, determined by calculating the number of Li + and Na + ions in the flow-electrode. The adsorption of cations by the ZIFs is also investigated using graphs and contour maps depicting the ZIF−cation interaction energy. Additionally, the simulation results are validated through experiments involving the quantification of cation concentration in the feed solution. The results indicate that Li + /Na + selectivity depends on the cation affinity of the ZIF. It is preferable to recover Li + ions from the flow-electrode than from the CEM. Moreover, cations require external energy to enter the pores as they experience repulsion. To achieve high Li + /Na + selectivity in the flow-electrode, the ZIF selective layers should exhibit a stronger affinity for Na + than for Li + . Additionally, the cavities at the surface of the ZIFs should be sufficiently small to restrict Na + entry. Overall, MD simulations are valuable for understanding the mechanisms necessary to achieve high Li + /Na + selectivity in ZIFs for FCDI applications. Among the three ZIFs tested, ZIF-8-Br exhibits the highest Li + /Na + selectivity in both simulations and experiments.