In this work, we prepared the nafion/montmorillonite/heteropolyacid nanocomposite membranes for direct methanol fuel cells (DMFCs). The analyses such as X-ray diffraction (XRD), Fourier transform infrared (FTIR), and scanning electron microscopy (SEM) were conducted to characterize the filler dispersion and membrane structure in prepared nanocomposite membranes. XRD patterns of nafion-CsPW-MMT nanocomposites membranes showed the exfoliated structure of membranes by adding MMT and CsPW. SEM-EDXA results showed proper dispersion of nanoparticles in the membrane matrices. Addition of CsPW-MMT to nafion membranes increases water uptake and IEC due to increase hydrophilic groups in membranes. The proton conductivity results showed that proton conductivity increases by increasing amount of CsPW and decreasing of clay content in the membrane. Methanol crossover through polymer electrolyte membranes is a critical issue and causes an important reduction of performance in DMFCs. The developed intercalated nafion/CsPW/MMT nanocomposite membranes have successfully improved the membrane barrier properties due to the unique feature of MMT which contributed to the formation of a longer pathway towards methanol across the membrane. The lowest methanol crossover of the developed membranes in this study was 1.651×10-6 cm2 s-1 which was lower than re-cast nafion membrane (2.078×10-6 cm2 s-1). The methanol permeability was significantly reduced by the incorporation of MMT and increased by addition of CsPW in the nafion membrane. Finally, according to the selectivity results, the nafion-MMT-CsPW nanocomposite membrane with MMT mass fraction of 2.5% and CsPW mass fraction of 8% shows the best membrane selectivity and this nanocomposite membrane could be suitable for application in DMFCs.