Electrodialysis (ED) is considered an effective technology for desalinating shale gas flowback fluid toward environmental risk control and resource recovery. However, membrane fouling remains a significant challenge and the particular fouling behavior of ion-exchange membranes (IEMs) in real scenario remains unclear. In this study, we employed interface characterization techniques including electrochemical impedance spectroscopy (EIS) to investigate the fouling behavior of both anion-exchange membranes (AEMs) and cation-exchange membranes (CEMs) during the desalination process. Notably, a positive correlation was observed between the transmembrane electric potential (TMEP) of the target membrane and the extent of membrane fouling during ED processing. EIS data revealed the membrane bulk exhibited the most pronounced increase in modeled electrical resistance, suggesting that internal fouling more significantly inhibited mass transfer compared to external fouling. Under varying current densities, the resistance of the AEM and CEM membrane bulk increased from an initial value of 3.93–16.53 Ω cm2 and from 3.90 to 9.87 Ω cm2, respectively, corresponding to their maximum TMEP increase by factors of 6.0 and 2.0 during the ED treatment. Our results demonstrate that AEM undergone a more severe organic fouling than CEM (scaling) during desalination of real shale gas flowback fluid. Effective strategies to mitigate the fouling issue in IEMs were finally proposed. These findings provide valuable guidance on future process optimizing and fouling mitigation in the ED treatment of real shale gas flowback fluid.