Exploitation of novel faradic electrode materials is an alternative implementation for solving the problem of poor specific electrosorption capacity that conventional carbon-based electrodes are encountered in capacitive deionization. Particularly, composite electrode is just an suitable choice because of its potentially high ion-storage ability. Herein, a cyclic voltammetric treatment method with different low limit of potential window were used to manipulate the polymeric conformation and doping level of graphene oxide/polypyrrole (GO/PPy) composite electrode. Based on it, the effect of polymeric structure on the electro-sorption performance was systematically studied. When the low limit of potential window is shifted to a potential negative enough, the irreversible polymeric conformational shrinks of GO/PPy electrode are promoted, which not only hinders the insertion process of ions in the composite matrix, but also decrease the doping level of polymer due to the intensive interchain interaction produced by more entangled polymeric chain. Thus, the number of intercalated ions should decrease, which is expressed by EIS results and is proportional to the electro-sorption capacity of GO/PPy composite electrode in MCDI process. Our work suggest that the less packing density, higher doping level and more charge delocalization on PPy backbone in composite electrode is beneficial to enhance its capacitive deionization performance.