Through nanochannels are created in the polymer/hybrid films by irradiating swift heavy ions followed by selective chemical etching of the amorphous latent track caused by irradiation. The dimensions of the nanochannels are varied from 30 to 100 nm by either using small (lithium) and large (silver) size of swift heavy ions with high energy (80 MeV) or by embedding few percentage of two-dimensional nanoparticle in the polymer matrix. The side walls of the nanochannels are grafted with polystyrene using the free radicals created during irradiation. Polystyrene graft is functionalized by tagging sulfonate group in the benzene ring of polystyrene to make the nanochannels conducting and hydrophilic. The proof of grafting and functionalization is shown through various spectroscopic techniques. The relaxation behavior and thermal stability of graft polymer within the nanochannel are shown through different thermal measurements. Nanoclay in nanohybrid nucleates the piezoelectric phase in the polymer matrix whose extent is further increased in grafted and functionalized specimen. Functionalized nanochannels exclusively facilitate proton conducting, whereas the remaining part of the film is electroactive, making it as a smart membrane. Greater water uptake, ion exchange capacity (IEC), high activation energy (8.3 × 10³ J mol^–1), and high proton conduction (3.5 S m^–1) make these functionalized nanohybrid film a superior membrane. Membrane electrode assembly has been made to check the suitability of these membranes for fuel cell application. Open circuit voltage and potential are significantly high for nanohybrid membrane (0.6 V) as compared to pure polymer (0.53 V). Direct methanol fuel cell testing using the membrane assembly exhibit a considerable high power density of ∼400 W m^–2, making these developed membranes suitable for fuel cell application and providing the ability to replace standard membrane like Nafion, as the methanol permeability is low, thus raising the higher selectivity parameter of the nanohybrid membrane.