Nafion series cation exchange membranes are extensively investigated and applied in proton exchange membrane fuel cells and flow battery technologies because of their excellent stability and easy availability. However, a deep understanding of their ions transport mechanism and behavior under the alkaline based flow battery media is very limited. Here, the ion transport mechanism through Nafion membrane under alkaline medium is investigated by small-angle X-ray scattering and atomic force microscope techniques. The results indicate that a membrane showed a higher degree of phase separation and larger cluster radius in a NaOH solution than those in a KOH solution, which endows the membrane with a much higher ion conductivity in the NaOH solution. Density functional theory-based simulation also indicates that the adsorption and desorption between the Na+ and the -SO3- in Nafion is faster than those of K+. Inspired by these results, an alkaline zinc iron flow battery with a Nafion 212 membrane using NaOH as the supporting electrolyte exhibits a coulombic efficiency of similar to 99% and an energy efficiency of similar to 86% at 80 mA cm(-2). This work offers insights into ways to obtain an improved battery performance for the existing as well as the emerging alkaline based flow battery technologies.