Nanocomposite membranes based on polyelectrolyte complex (PEC) of chitosan/phosphotungstic acid (PWA) and different types of montmorillonite (MMT) were prepared as alternative membranes to Nafion for direct methanol fuel cell (DMFC) applications. Fourier transform infrared spectroscopy (FTIR) revealed an electrostatically fixed PWA within the PEC membranes, which avoids a decrease in proton conductivity at practical condition. Various amounts of pristine as well as organically modified MMT (OMMT) (MMT: Cloisite Na, OMMT: Cloisite 15A, and Cloisite 30B) were introduced to the PEC membranes to decrease in methanol permeability and, thus, enhance efficiency and power density of the cells. X-ray diffraction patterns of the nanocomposite membranes proved that MMT (or OMMT) layers were exfoliated in the membranes at loading weights of lower than 3 wt.%. Moreover, the proton conductivity and the methanol permeability as well as the water uptake behavior of the manufactured nanocomposite membranes were studied. According to the selectivity parameter, ratio of proton conductivity to methanol permeability, the PEC/2 wt.% MMT 30B was identified as the optimum composition. The DMFC performance tests were carried out at 70 A degrees C and 5 M methanol feed and the optimum membrane showed higher maximum power density as well as acceptable durability compared to Nafion 117. The obtained results indicated that owing to the relatively high selectivity and power density, the optimum nanocomposite membrane could be considered as a promising polyelectrolyte membrane (PEM) for DMFC applications.