A novel composite membrane was prepared by incorporation of phosphotungstic acid (PWA) and silicotungstic acid (SWA) into sulfonated polystyrene ethylene butylene polystyrene (SPSEBS) by solution casting method. The interactions of SPSEBS with heteropoly acids (HPA) were studied by Fourier transform infrared (FTIR). From the thermogravimetric analysis (TGA), the thermal stability of the composite membranes was found to be increased with increased inorganic content and the X-ray diffraction study proved the crystalline structure of HPA in the membrane. SEM and AFM images of composite materials showed evidence uniform distribution of HPA in SPSEBS. The IEC and proton conductivity of the composite membranes increased with the increase in HPA content and in contrast the water absorption, methanol absorption and methanol permeability values decreased with increasing HPA. The performance of the SPSEBS and composite membranes was studied and compared with Nafion 117 in both proton exchange membrane fuel cells (PEMFC) and direct methanol fuel cells (DMFC) single cell setup.