Tremendous efforts have been dedicated to developing sustainable and affordable ion exchange membranes for flow batteries. Challenges remain in terms of high cost, low coulombic efficiency caused by the crossover of active species, and stability. Inspired by the highly hydrophilic and interconnected 3D networks of nanofibers of bacterial cellulose (BC), an unprecedented ion exchange membrane possessing high ionic selectivity is created by impregnating a hydrophobic copolymer poly(vinylidene fluoride-co-hexafluoropropylene) (PVDF-HFP) into BC aerogel scaffolds. The high proton conductivity of the membrane stems from the intrinsically high hydrophilic network of the BC fibrils, which offers a percolated pathway for the proton conduction. At the same time, the selectivity arises from the hydrophobic lamination on the BC scaffold that acts as a barrier for the migration of vanadium ions and reduces its crossover. Therefore, the hydrophilic ion transport paths of BC inside of a stable PVDF-HFP matrix result in a high proton conductivity of 0.0095 S cm−1 at 25 °C and a significantly less vanadium permeation rate. Besides, the membrane yields a high tensile strength of 114 MPa and excellent thermal stability. Moreover, vanadium redox flow battery assembled using the BC/PVDF-HFP membrane demonstrated cyclings for 300 continuous cycles at a constant current density of 100 mA cm−2 and achieved an average coulombic efficiency of 97.56%, voltage efficiency of 81.56%, and energy efficiency of 79.49%. The higher CE, and, therefore, energy efficiency of the BC/PVDF-HFP membrane than those of the Nafion 115 can be attributed to the natural percolated 3D networks of BC.