In this study, poly(3,4-propylenedioxythiophene)/TiO2 nanorod modified with 3-aminopropyltriethoxysilane (APTES)/FTO electrodes and for comparision poly(3,4-alkylenedioxythiophene)/FTO (fluoride tin oxide) were produced by using an electrochemical deposition method. The surface roughness of these electrodes were characterized by AFM measurement and morphological effect on electrocatalytic ability for triiodide (I-3(-)) reduction were investigated. We found that catalytic activity become better with increasing roughness of the electrode surfaces. Electrochemical impedance spectroscopy (EIS) measurements within a symmetrical polymer/I-3(-)/I-/polymer cell were carried out in order to understand impedance properties of these electrodes. Cyclic voltammetry and EIS results of electrodes indicated that the poly(3,4-propylenedioxythiophene)/modified TiO2 nanorod/FTO electrode shows better catalytic activity towards I-/I-3(-) redox reaction than that of poly(3,4-alkylenedioxythiophene)/FTO electrodes. In addition, we showed that the modification of TiO2 surfaces with 3-aminopropyltriethoxysilane provides to improve the contact between TiO2 and poly(3,4-propylenedioxythiophene) thus increasing in electrocatalytic ability for I-3(-) reduction.