In the present research, proton exchange membranes based on partially sulfonated poly (ether sulfone) (S-PES) with various degrees of sulfonation were synthesized. It was found that the increasing of sulfonation degree up to 40% results in the enhancement of water uptake, ion exchange capacity and proton conductivity properties of the prepared membranes to 28.1%, 1.59 meq g −1 , and 0.145 S cm −1 , respectively. Afterwards, nanocomposite membranes based on S-PES (at the predetermined optimum sulfonation degree) containing various loading weights of organically treated montmorillonite (OMMT) were prepared via the solution intercalation technique. X-ray diffraction patterns revealed the exfoliated structure of OMMT in the macromolecular matrices. The S-PES nanocomposite membrane with 3.0 wt% of OMMT content showed the maximum selectivity parameter of about 520,000 S s cm −3 which is related to the high conductivity of 0.051 S cm −1 and low methanol permeability of 9.8 × 10 −8 cm 2 s −1 . Furthermore, single cell DMFC fuel cell performance test with 4 molar methanol concentration showed a high power density (131 mW cm −2 ) of the nanocomposite membrane at the optimum composition (40% of sulfonation and 3.0 wt% of OMMT loading) compared to the Nafion ® 117 membrane (114 mW cm −2 ). Manufactured nanocomposite membranes thanks to their high selectivity, ease of preparation and low cost could be suggested as the ideal candidate for the direct methanol fuel cell applications.