Through channels in thin polymer/nanohybrid films have been made by irradiating with high energy swift heavy ions (SHI) followed by selective chemical etching of the amorphous zone in the latent track created by SHI during the bombardment. The average size of the nanochannels (30–65 nm) was controlled by varying the fluence of SHI along with the nanohybrid preparation of the polymer, by dispersing a few percent of two-dimensional nanoclay in the matrix. Grafting was applied within the nanochannels through polymerization of conducting poly(3-hexyl thiophene) which was further functionalized to make the channels ion conducting. Nanoclay alters the crystalline phase to the piezoelectric all-trans β-phase in the nanohybrid whose extent has increased further after irradiation, grafting and sulphonation. Structural alteration has also been reflected in its thermal behavior (similar melting behavior in the pure polymer against the considerably higher melting point in the functionalized nanohybrid). The bulk dc conductivity of the functionalized membrane increased 13 orders of magnitude compared to the unirradiated specimens and activation energies also increased for the functionalized hybrid membrane (20 and 32 kJ mol⁻¹ for the functionalized pure polymer and its nanohybrid, respectively) suggesting better stability of the functionalized membranes at higher temperature. Water uptake and proton conductivities of the functionalized hybrid membranes are similar to those of the standard Nafion membrane while the higher selectivity parameter along with significantly lower methanol permeability of the functionalized hybrid membrane strongly suggests that it is a better membrane for fuel cell applications. A membrane electrode assembly has been prepared to measure the performance of direct methanol fuel cells indicating a significantly higher value of power density of the developed functionalized hybrid membranes.