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Proton-conducting membranes were fabricated from a new short-side chain ionomer Inion (Russian analogue of Aquivion) by solution casting method. A series of temperature treatment experiments was conducted to show that annealing of Inion membranes at the temperature range from 160 °C to 170 °C leads to a significant increase of specific proton conductivity to values even higher than those of commercial membrane Nafion NR212. An explanation of this fact can be given by considering the membranes’ proton transport mechanism and water behavior models in nanopores. Matching the proton conductivity mechanism of the membranes, which is realized in nanostructured channels with the diameter of about several nanometers according to the Grotthuss proton hopping mechanism, and the model of water and ice states in nanopores leads to the comprehensive understanding for the further optimization of the membranes to achieve high transport characteristic. For example, it can be improved by increasing the number of side-chain branches of the polymer.