The high proton conductivity of Nafion© membranes in direct methanol fuel cells is attributed to a random three dimensional 3D network of elongated ion channels formed by bundles of rod-like inverted micelles. However, this network is also responsible for high methanol crossover. In addition, its conductivity is impaired at temperatures 120 °C and above due to ion channel rearrangement, thus limiting the operational temperature to 60–80 °C. Here we report a composite proton exchange membrane prepared by filling the pores of polycarbonate track-etched membrane with Nafion, which promote channel orientation roughly normal to the surface. The proton conductivity of this geometry is significantly enhanced, presumably due to the restricted swelling, resulting in a better ion channel connectivity and realignment in the axial pore direction upon hydration. The permeability of sodium chloride and methanol, though, is suppressed, presumably due to formation of regions of closely packed sulfonic groups, which facilitate proton transfer but strongly exclude other solutes. Composite membranes with improved conductivity and selectivity based on the principle presented here are expected to allow operating direct methanol fuel cells at higher temperatures and with higher methanol concentrations, thus reducing costs and increasing the efficiency.