In vanadium redox flow batteries (VRFBs), a perfluorinated sulfonic acid (PFSA) ionomer membrane plays a crucial role in transporting ions through hydrophilic channels. However, its randomly interconnected channels with relatively large size in a hydrated state cause low proton/vanadium ion selectivity, imposing a limitation in enhancing performance of VRFB. Herein, we develop an ultrathin PFSA membrane of highly aligned ion channels with reduced size, by molecular arrangement on the air/water interface. Well-ordered ion channels dramatically suppress the vanadium ion crossover, enhancing 500-fold in the ion selectivity compared to conventional PFSA membranes. The molecularly controlled ultrathin PFSA membranes exhibit stable cell performance on a porous support over various current densities and long-term cycles (800 cycles), exceeding the energy efficiency of Nafion 211 (73%) at 200 mA/cm(2). Highly ordered ultrathin PFSA membranes with high ion selectivity could offer a practically applicable low-cost, yet high-performance membrane for VRFBs.