We explore an approach to effectively enhance the properties of cost-effective hydrocarbon protonexchange membranes for application in the direct methanol fuel cell (DMFC). This approach utilizes sulfonated silica nanoparticles (SA-SNP) as additives to modify sulfonated poly(arylene ether ether ketone ketone) (SPAEEKK). The interaction between the sulfonic acid groups of SA-SNP and those of SPAEEKK combined with hydrophilic-hydrophobic phase separation induce the formation of proton conducting channels, as evidenced by TEM images, which contribute to increases in the proton conductivity of the SPAEEKK/SA-SNP nanocomposite membrane. The presence of SA-SNP nanoparticles also reduces methanol crossover in the membrane. Therefore, the SPAEEKK/SA-SNP nanocomposite membrane shows a high selectivity, which is 2.79-fold the selectivity of Nafion ® 117. The improved selectivity of the SPAEEKK/SNP nanocomposite membrane demonstrates potential of this approach in providing hydrocarbon-based PEMs as alternatives to Nafion in direct methanol fuel cells.