High conductivity and selectivity are required properties for membranes for flow batteries. Unfortunately, there is often a tradeoff between the two. We have developed a hierarchically structured cation exchange membrane by integrating a dense, crack-free tungsten oxide coating layer on Nafion. The Nafion layer is also infiltrated with tungsten oxide in its hydrophilic, ion cluster regions. The composite structure is essential to maintaining a stable interface between the oxide coating layer and Nafion. The formation of oxide inside the Nafion hydrophilic region reduces water uptake and swelling ratio. The dimensionally stable composite layer thus serves as a stable support for the dense oxide coating on top. Coated by a sol-gel method, the dense oxide layer selectively transports cations (proton and potassium). Combing these two components of the structure results in a hierarchical structure with mechanical stability, high conductivity, and excellent selectivity. The permeability for Fe(II) and Cr(III) ions through the membrane are 2.31×10^-8 cm²s^-1 and 8.34×10^-9 cm²s^-1 respectively, an order of magnitude lower than Nafion, while the conductivity is comparable. Furthermore, the top dense oxide layer is estimated to exhibit a permeability for multivalent cations of only less than 0.2% of Nafion. The hierarchical structure design is a promising candidate for flow battery membrane applications.