Recently, we have reported a new all tungsto-cobalt heteropoly acid redox flow battery (all H6[CoW12O40] RFB) with high coulombic efficiency. Because of the relatively large ion size and high negative charge, the tungsto-cobalt heteropoly acid anion is difficult to cross Nafion membrane, which makes it possible to employ thinner Nafion membrane in all H6[CoW12O40] RFB. In this study, three types of Nafion membranes with different thickness, namely, N212 (50 μm), N211 (25 μm), and N-17 (home-made, 17 μm) are used as polymer electrolyte to investigate its effects on the performance of all H6[CoW12O40] RFB. The ion permeability increases while the area specific resistanceas decreases as reducing the membrane thickness. As a result, the RFB with N211 membrane exhibits best comprehensive performance, which exhibites the energy efficiency of 88.6% at current density of 0.10 A cm−2 and the power density of 0.56 W cm−2 at 0.60 A cm−2. Moreover, the battery delivers impressive cycling performance of 100 cycles with an average coulombic efficiency of 99.4%, energy efficiency of 80.0%, and capacity retention of 99.98% per cycle at current density of 0.20 A cm−2.