An amphoteric ion-exchange membrane (AIEM) from fluoro-methyl sulfonated poly(arylene ether ketone) bearing content-controlled benzimidazole moiety, was firstly fabricated for vanadium redox flow battery (VRB). The AIEM and its covalently cross-linked membrane (AIEM-c) behave the highly suppressed vanadium-ion crossover and their tested VO2+ permeability are about 638 and 1117 times lower than that of Nafion117, respectively. This is further typically verified by the lower VO2+ concentration inside AIEM that is less than half of that inside Nafion117 detected by energy dispersive X-ray spectrometry, in addition of the nearly 3 times longer battery self-discharge time. The ultra-low vanadium ion diffusion could be ascribed to the narrower ion transporting channel originated from the acid-base interactions and the rebelling effect between the positively-charged benzimidazole structure and VO2+ ions. It is found that, VRB assembled with AIEM exhibits the equal or higher Coulombic efficiency (99.0% vs. 96.4%), voltage efficiency (90.7% vs. 90.7%) and energy efficiency (89.8% vs. 87.4%) than that with Nafion117 and keeps continuous 220 charge–discharge cycles for over 25 days, confirming that the AIEM of this type is a potentially suitable separator for VRB application.