AbstractNafion® and Montmorillonite (MMT) functionalized with Krytox nanocomposite membrane (Krytox–MMT–Nafion®) is proposed for DMFC applications. The nanocomposite is obtained with good compatibility between MMT and Nafion® via the function of Nafion®-like polymer chain namely Krytox 157 FSL. The MMT layers are exfoliated with Nafion® polymer matrices and show homogeneity as confirmed by XRD and SEM. The AFM micrographs clarifies the successful MMT clay dispersion all over the nanocomposite membrane. The thermogravimetric analysis exhibits the improvement in water retention and thermal resistance as compared to Nafion® membrane. The membranes perform for more than 50% reduction in the permeation of methanol in 10%(v/v) solution at either room temperature or as high as 60 °C. The Arrhenius plot suggests the lower activation energy for proton migration in the Krytox–MMT–Nafion® membranes than in the Nafion® membrane under Grotthus mechanism.