Porous organic frameworks (POFs), including metal‐organic frameworks (MOFs) and covalent organic frameworks (COFs), have drawn attention as ion‐selective materials due to their well‐defined channels and functional sites. However, their individual limitations require novel approaches to maximize their potential. In this study, a hybrid bilayer membrane combining MOFs and COFs on a nylon substrate via consecutive liquid‐liquid interface polymerization is developed. This method forms robust chemical bonds between the MOF and COF layers, creating efficient ion transport channels. The integration of ZIF‐8 (MOF layer), which exhibits strong electrostatic repulsion against cations, with TpPa‐SO3H (COF layer), offering strong cation coordination, results in a synergistic effect that significantly enhances ion separation. The ZIF‐8/TpPa‐SO3H/nylon membrane achieved a Li+/Mg2+ separation ratio of 501, which is 400 times higher than the pristine ZIF‐8 membrane and 200 times higher than the TpPa‐SO3H membrane. This outstanding performance is due to the combined electrostatic repulsion of the MOF layer and functional coordination of the COF layer, enabling precise ion discrimination. The membrane's structural integrity and chemical stability further contribute to its superior ion separation efficiency, making it a promising candidate for large‐scale lithium extraction from salt lakes.