As the share of sustainable energy sources in the electricity supply rises, large-scale energy storage becomes increasingly important. All vanadium flow batteries, as one of the most promising large-scale energy storage methods, have reached the commercialization stage because of their unique feature of uncoupling power and energy, as well as the advantages of long life, high safety, and low cost. The ion-selective membrane is an essential part of flow batteries, which allows specific ions to pass through to maintain a neutral charge and prevents the crossover of active species to maintain the capacity. However, the high cost and low ion-selectivity of the commercialized ion-selective membranes (i.e., Nafion membranes) hindered the further promotion of the flow batteries. Herein, we developed a large scalable double-layer ion selectivity membrane with a unique bifunctional nanoporous boron nitride (PBN) ion selective layer and a low-cost porous polyetherimide (PEI) ion conductivity and support layer. PBN was synthesized by a large scalable template-free method, which was further decorated with Nafion resin. The nano-sized and tortuous pores of the PBN can effectively block the crossover of vanadium ions and provide excellent ion selectivity based on the pore size exclusion mechanism. Furthermore, the super-acidic sulfonic acid groups of Nafion decorated on the nanoporous structure of PBN provide high-speed proton transfer channels that increase proton conductivity through both Grotthuss and vehicle mechanisms. The low-cost porous PEI ion conductivity and support layer was prepared by the phase separation method. The well-aligned asymmetric finger-like porous structure of the PEI membrane provides excellent ion conductivity. The addition of a hydrophilic polymer additive, polyvinylpyrrolidone, further increased its ion conductivity. The PBN–PEI double layer membrane, prepared by a simple spray coating method, demonstrated an excellent ion selectivity (1.49×108 mS cm−3 min), which is almost 15 times higher than that of the pristine PEI membrane (6.71×106 mS cm−3 min) while maintaining high ion conductivity (64 mS cm−1). The PBN–PEI membrane achieved superior performance (97% of coulombic efficiency, 94% of voltage efficiency, and 91% of energy efficiency at 40 mA cm−2) than the Nafion 115 membrane in the all-vanadium flow battery with higher discharge capacity at all current densities and high stability with a lower capacity fading rate (0.17% per cycle vs. 0.74% per cycle at 100 mA cm−2). The PBN–PEI membrane also demonstrated a stable operation in the all-vanadium flow battery at a current density of 100 mA cm−2 over 700 cycles. The work presented the remarkable performance of the ultra-thin PBN bifunctional layer in terms of ion conductivity and selectivity; the combination with the low-cost high ion-conductive porous PEI membrane and a simple fabrication process demonstrated a great potential for commercialization of the PBN-PEI double-layer membrane.