Proton exchange membranes with remarkable performance are important for the development of direct methanol fuel cells. Inspired by the proton-conducting mechanism of transmembrane proteins, amino-acid-functionalized cellulose whiskers, are developed as a novel proton-conducting pathway for hybrid proton exchange membranes. Fmoc-amino acids are immobilized onto the surface of cellulose whiskers to obtain amino acids (Glycine, 5-amino-Valeric acid, L-Serine, L-Asparagine, and L-Leucine) functionalized cellulose whiskers with primary amino groups after Fmoc-deprotection. Proton-conducting mixed-matrix membranes are obtained by incorporating amino-acid-functionalized cellulose whiskers into sulfonated polysulfone. The performance of hybrid proton exchange membranes is evaluated to study the effects of the structure and content of amino acids. Results shows that the introduction of amino acids considerably enhances the proton conductivity. Proton exchange membranes with 4 wt.% and 10 wt.% content of L-Serine-functionalized cellulose whiskers have high proton conductivity of 0.209 S/cm and 0.234 S/cm at 80 degrees C, respectively. In addition, water uptake, resistance to methanol permeability and single-cell performance are also enhanced. These results indicates that the composition of filler and mixed matrix exhibit remarkable properties, and proton-conducting mixed-matrix membranes are promising materials in direct methanol fuel cells.