This paper presents an improved impregnation–reduction (I–R) method for modifying a Nafion membrane that achieves a lower methanol crossover. During impregnation of the Nafion membrane in Pd(NH3)4Cl2 solution, an electric field was conducted across the membrane to enhance the migration of Pd ions. After impregnation, Pd ions were reduced to form Pd nanoparticles by soaking the membrane in NaBH4 solution. The test results show that the Pd–Nafion membrane prepared by the improved I–R method has higher proton conductivity and lower methanol permeability than that prepared by usual I–R method.