In order to enhance the ion adsorption capacity and ion selective ability of electrode materials, carbon nanotube/polypyrrole (CNT/PPy) composites doped with chloride (Cl-) and dodecyl benzene sulfonate (DBS-) were used for capacitive deionization (CDI) process, respectively. Seven types of symmetric and asymmetric CDI cells based on the obtained composite electrodes and CNT electrode were assembled and tested. The experimental results indicated that the desalination performance for CDI cells typically depended on the potential of zero charge (PZC) of the electrodes and the potential distribution of the cells. The PZC of the CNT, CNT/PPy-Cl and CNT/PPy-DBS electrodes were measured to be 0 V, -0.1 V and 0.4 V vs. saturated calomel electrode, respectively. In the applied potential of 1.2 V, the largest effective working potential of 1.2 V and the highest adsorption capacity of 35.46 mg/g were found based on the CNT/PPy-Cl (anode)||CNT/PPy-DBS (cathode) cell, in which the PZCs were all outside of the polarization window of the corresponding electrodes. While a diminished effective working potential and desalination performance can be observed when one of the PZCs at least was within the polarization window of the respective electrode. This work provides an effective approach for optimizing electrode configuration based on PZC analysis.