Based on a previously developed polyamide proton conductive macromolecule, the nano-scale structure of the self-assembled proton conductive channels (PCCs) is adjusted via enlarging the nano-scale pore size within the macromolecules. Hyperbranched polyamide macromolecules with different size are synthesized from different monomers to tune the nano-scale pore size within the macromolecules, and a series of hybrid membranes are prepared from these two micromoles to optimize the PCC structure in the proton exchange membrane. The optimized membrane exhibits methanol permeability low to 2.2 × 10−7 cm2/s, while the proton conductivity of the hybrid membrane can reach 0.25 S/cm at 80 °C, which was much higher than the value of the Nafion 117 membrane (0.192 S/cm). By considering the mechanical, dimensional, and the thermal properties, the hybrid hyperbranched polyamide proton exchange membrane (PEM) exhibits promising application potential in direct methanol fuel cells (DMFC).