NaA zeolite membrane is an ideal hydrophilic candidate for organic dehydrations; however, its instability in salt solutions limits its application in industries as the membrane intactness was greatly affected due to the replacement of cation ions. In order to explore the relationship between the structural variation and the cation types, the obtained NaA zeolite membranes were treated by various monovalent and divalent cations like Ag⁺, K⁺, Li⁺, NH₄⁺, Zn2+, Mg2+, Ba2+ and Ca2+. The obtained membranes were subsequently characterized by contact angle, scanning electron microscopy (SEM), pervaporation (PV), and vapor permeation (VP). The results showed that all of the hydrophilicities of the exchanged membrane were reduced, and the membrane performance varied with cation charges and sizes. For the monovalent cations, the membrane performance was largely determined by the cation sizes, where the membrane remained intact. On the contrary, for the divalent cation treatments, the membrane separation was generally reduced due to the presence of cation vacancies, resulting in some unbalanced stresses between the dispersive interaction and electrostatic forces, thereby damaging the membrane intactness. In the end, a set of gas permeation experiments were conducted for the two selected cation-treated membranes (K⁺ and Ag⁺) using H₂, CO₂, N₂ and CH₄, and a much higher decreasing percentage (90% for K⁺) occurred in comparison with the permeation drop (10%) in the PV dehydration, suggesting that the vaporization resistance of phase changing for the PV process was more influential than the water vapor transport in the pore channel.