A membrane with a low methanol permeability and high proton conductivity (σp) is essential for the effective operation of a direct methanol-based fuel cell. Herein, a bio-metal organic framework was prepared with natural α-amino acids as ligands and then combined with hydrolyzed polyacrylonitrile (PAN) nanofibers (AA-MOF@PAN). The resulting nanocomposite membranes were subsequently integrated into a Nafion matrix (AA-MOF@PAN/Nafion). The –NH2 groups on AA-MOF@PAN interact with –SO3H groups on Nafion, forming long-range acid-base pairs along the interface between the matrix and nanofibers. This interaction creates abundant proton-conducting sites for proton exchange membrane. Notably, the AA-MOF@PAN-4h/Nafion membrane demonstrated an exceptional proton conductivity (σp) of 0.25 S cm−1 and a higher power density of 117.61 mW cm−2 compared to the recast Nafion membrane. This study offers valuable insights into the three-dimensional ordered design of a natural α-amino acids as a proton transfer sites and highlighting their potential applications in proton exchange membranes.