In capacitive deionization (CDI), the functionalization or modification of carbon electrodes and the mitigation of positive electrode oxidation are effective methods to improve desalination capacity and stability for practical application. Here, the covalent bond attached three-dimensional (3D) graphene/carbon nanotubes hybrid (G-CNTs) with rich conductive channels was chosen as electrode material, and a periodically alternated (positive and negative) voltage operation (1.2/0/-1.2/0 V) was applied that aims to enhance the efficiency and stability of capacity deionization. The desalination capacity of the G-CNTs electrode increased gradually over the first few cycles in this operation, while the usage cycle of CDI could be pronouncedly extended almost six times, compared with the CDI of regular applied voltage operation (1.2/0 V). Through the characterization of electrode and CDI cell, this enhancement of the desalination performance is attributed to the synergistic benefits of alternating oxidation of negative and positive electrode, which can mitigate the oxidation of the positive electrode as well as achieve negative surface charge enhanced negative electrode. Therefore, a periodically alternated voltage operation is an economical and efficient method to control the oxidation of electrodes for enhancing the desalination performance.