<p>Development of high-performance ion-selective membranes is crucial for achieving efficient ion separation in water treatment and energy storage applications. In this study, we demonstrate the strategic incorporation of acid-base pairs within a polybenzimidazole matrix through controlled sulfonation. By leveraging these intermolecular interactions, we enhance the Li⁺/Mg²⁺ selectivity of the membrane. At an optimal sulfonation degree, the SP45 membrane forms a cross-linked structure, featuring contracted ionic clusters and discrete hydrophilic domains with limited interconnectivity. This unique microstructure imposes significantly higher energy barriers for the transmembrane transport of Mg²⁺, thereby endowing the SP45 membrane with exceptional perm-selectivity of 48.1 at a current density of 2 mA cm⁻². Cycling stability tests reveal that the Li⁺/Mg²⁺ selectivity degradation remains below 10% across multiple cycles in diverse mixed-salt systems. In practical brine ion distillation tests, we achieved a separation factor of exceeding 60,000 between Li⁺ and Mg²⁺ utilizing a 4-stage ion-distillation device equipped with the prepared SP45 membranes. This work provides fundamental insights into ion transport regulation through molecular-level acid-base pairs engineering, opening new avenues for advanced ion-selective separation membranes.</p>