Membranes of high ion permselectivity are significant for the separation of ion species at the subnanometer scale. Here, we report porous organic cage (i.e., CC3) membranes with hierarchical channels including discrete internal cavities and cage-aligned external cavities connected by subnanometer-sized windows. The windows of CC3 sieve monovalent ions from divalent ones and the dual nanometer-sized cavities provide pathways for fast ion transport with a flux of 1.0 mol m-2 h-1 and a mono-/divalent ion selectivity (e.g., K+/Mg2+) up to 103, several orders of magnitude higher than the permselectivities of reported membranes. Molecular dynamics simulations illustrate the ion transport trajectory from the external to internal cavity via the CC3 window, where ions migrate in diverse hydration states following the energy barrier sequence of K+ < Na+ < Li+ ≪ Mg2+. This work sheds light on ion transport properties in porous organic cage channels of discrete frameworks and offers guidelines for developing membranes with hierarchical channels for efficient ion separation.