AbstractProtein channels on the biofilm conditionally manipulate ion transport via regulating the distribution of charge residues, making analogous processes on artificial membranes a hot spot and challenge. Here, we employ metal–organic frameworks (MOFs) membrane with charge‐adjustable subnano‐channel to selectively govern ion transport. Various valent ions are binded with crown ethers embedded in the MOF cavity, which act as charged guest to regulate the channels’ charge state from the negativity to positivity. Compared with the negatively charged channel, the positive counterpart obviously enhances Li+/Mg2+ selectivity, which benefit from the reinforcement of the electrostatic repulsion between ions and the channel. Meanwhile, theoretical calculations reveal that Mg2+ transport through the more positively charged channel needed to overcome higher entrance energy barrier than that of Li+. This work provides a subtle strategy for ion‐selective transport upon regulating the charge state of insulating membrane, which paves the way for the application like seawater desalination and lithium extraction from salt lakes.