Covalent organic frameworks (COFs) have emerged as promising platforms for membrane separations, while remaining challenging for separating ions in a fast and selective way. Here, we propose a concept of COF membranes with vertically aligned nanorods for efficient separation of rare metal ions. A quaternary ammonium-functionalized monomer is rationally designed to synthesize COF layers on porous substrates via interfacial synthesis. The COF layers possess an asymmetric structure, in which the upper part displays vertically aligned nanorods, while the lower part exhibits an ultrathin dense layer. The vertically aligned nanorods enlarge contact areas to harvest water and monovalent ions, and the ultrathin dense layer enables both high permeability and selectivity. The resulting membranes exhibit exceptional separation performances, for instance, a Cs+ permeation rate of 0.33 mol m−2 h−1, close to the value in porous substrates, and selectivities with Cs+/La3+ up to 75.9 and 69.8 in single and binary systems, highlighting the great potentials in the separation of rare metal ions.