Commercializing direct methanol fuel cells (DMFC) demands cost-effective cation exchange membranes. Herein, a polymeric blend is prepared from low-cost and eco-friendly polymers (i.e., iota carrageenan (IC) and polyvinyl alcohol (PVA)). Zirconium phosphate (ZrPO4) was prepared from the impregnation–calcination method and characterized by energy dispersive X-ray analysis (EDX map), X-ray diffraction analysis (XRD), Fourier transform infrared spectroscopy (FTIR), and transmission electron microscopy (TEM), then incorporated as a bonding and doping agent into the polymer blend with different concentrations. The new fabricated membranes were characterized by SEM, FTIR, thermogravimetric analysis (TGA), differential scanning calorimetry (DSC), and XRD. The results revealed that the membranes’ physicochemical properties (oxidative stability, tensile strength) are enhanced with increasing doping addition, and they realized higher results than Nafion 117 because of increasing numbers of hydrogen bonds fabricated between the polymers and zirconium phosphate. Additionally, the methanol permeability was decreased in the membranes with increasing zirconium phosphate content. The optimum membrane with IC/SPVA/ZrPO4-7.5 provided higher selectivity than Nafion 117. Therefore, it can be an effective cation exchange membrane for DMFCs applications.