Abstract Ion transport in environments with mixed ions is crucial for numerous real‐world applications. However, most membranes suffer from reduced selectivity in the mixed ion environment. Herein, the concept of dual‐nanoconfined channels in covalent organic frameworks (COFs) is demonstrated for superior mixed mono‐/multivalent ion separation. By incorporating acidic functionalities into the pore wall and coupling with a suitable pore size in the COF membranes, multivalent ions interact strongly with the acidic groups. This shields the interactions of the wall with monovalent ions, leaves sufficient space for fast monovalent ion passage, and in the meantime blocks multivalent ions, creating well‐defined dual‐nanoconfinement for mixed ion separation. Consequently, mixed Li + /Mg 2+ ion selectivity exceeding 1,300 and mono‐/trivalent ion selectivity over 9,000 is achieved. Molecular dynamics simulation and experiment with multiple ion pairs further confirm the mechanisms. The study sheds light on a fundamentally new design principle for mixed ion separation, offering the potential to reach remarkable selectivity in practical applications.