In this work, electrochemical impedance spectroscopy (EIS) was utilized to probe interfacial structures of antifouling anion exchange membranes (AEMs) with different modifying architectures fabricated by graphene oxide (GO) and polydopamine (PDA). Results showed that the GO@PDA modified AEMs with a compact GO@PDA layer exhibited a new interface between the modifying layer and membrane matrix, different from the loose GO-modified AEMs. After fouling experiments, from quantifying electrical equivalent circuits fitted to EIS results, it could be found that GO-modified AEMs and PDA-modified AEMs exhibited a significant foulants layer, although the modifying layer reduced the amount of foulants absorbed in the membrane matrix. For GO@PDA-modified AEMs, the increase in ohmic resistance and the foulants layer was almost negligible. Only a small amount of foulants accumulating on the GO@PDA layer affected the capacitive resistance of the interfacial layer obviously. It was concluded that the electrochemical properties and interface of modified AEMs was influenced by the structure of modifying layer, and a dense and compact modifying layer could be more effective to block the foulants from depositing on the surface of AEMs and entering the membrane matrix. The electrochemical characterizations helped to elucidate the antifouling mechanism of modified AEMs with different structures and get a good understanding of the correlation among the properties, structures, and antifouling performance of the modifying layer.