An ultra-high ion-selective Nafion composite membrane modified by phosphotungstic acid (PWA) coupled silica for vanadium redox flow battery (VRB) was constructed and prepared through solution casting. The composite membrane exhibits excellent proton conductivity and vanadium ions blocking property by incorporating the nanohybrid composed of silica and PWA into the Nafion ionomer. Simple tuning for the filling amount of the nanohybrid endows the obtained membranes preeminent vanadium barrier property including a minimum vanadium permeability of 3.13 × 10−7 cm2 min−1 and a maximum proton conductivity of 0.081 S cm−1 at 25 °C. These indicate an ion selectivity of 2.59 × 105 S min cm−3, which is 6.8 times higher than that of recast Nafion (0.33 × 105 S min cm−3). As a result, the VRB with the composite membrane shows superior battery performance containing a lower self-discharge rate, higher capacity retention and more robust cyclic stability compared with recast Nafion over a range of current densities from 40 to 100 mA cm−2.