To develop new cost-effective and high performance ion exchange membranes (IEMs) for redox flow battery applications, poly(arylene ether sulfone) random copolymer membranes (BPSHs) with surface nano-crack coatings (P-BPSH) were prepared using a hydrophobic atmospheric plasma treatment. The effect of the nano-cracks on the membranes' ion transport properties and the performance of the vanadium redox flow batteries (VRFBs) were evaluated to better understand the feasibility of using this technique in membrane ionic selectivity. The ion-selective nano-crack surface significantly improved the proton selectivity, from 32.95 to 74.20, over vanadium (VO2+) ions. Consequently, the VRFB cell assembled using a P-BPSH-60 membrane showed higher coulombic and energy efficiencies compared to a VRFB with a pristine BPSH-60 membrane. The energy efficiency of the P-BPSH-60 membrane (85.37%) is comparable to that of a Nafion (R) 117 membrane (85.11%). The improved battery performance demonstrated that the surface nano-crack coating layer effectively blocked the transport of vanadium ions through the IEM without distinct reduction of the proton conductivity. The results suggest a promising strategy to enhance membrane proton selectivity over vanadium ions.