Nafion-115 nanowire arrays are synthesized with an extrusion method using AAO membranes as templates. It is indicated that the vacuum treating of AAO templates before surface decoration plays an important role in obtaining high filling rate of the Nafion-115 nanowires in the AAO templates, while the concentration of Nafion-115 DMSO solutions does not affect the filling rate greatly. The optimized parameters to synthesize the Nafion-115 nanowire arrays are studied. The filling rate of the Nafion-115 nanowires in the AAO templates synthesized with the optimized parameters is about 95%. The growth mechanism of Nafion-115 nanowires is discussed to qualitatively explain the experimental results.