The physicochemical and structural properties of the AMX (homogeneous AEM), AMA (semi-homogeneous AEM) and HAEM (heterogeneous AEM) were characterized systematically to examine their effects on membrane fouling from sodium dodecyl sulfate (SDS) in electrodialysis. Results demonstrated that the fouling of three AEMs was closely related to their membrane structure, and the denser membrane structure caused more SDS accumulated on the membrane surface to make the severer membrane fouling. The existence of SDS in the dilute solution caused the desalination rate of AMX, AMA and HAEM decreased by 42.3%, 15.3% and 9.2%, respectively. Different fouling layer was formed on the surface of AMX and AMA except HAEM, which was demonstrated firstly by element mapping of membrane cross-section. Electrochemical impedance spectroscopy (EIS) suggested the ionic migration through the fouled AMX was restricted completely, different from the trans membrane migration of partial ions through the fouled AMA and HAEM. Compared with the fouled AMA and HAEM, the performance of the fouled AMX caused by SDS was more difficult to be recovered due to its denser membrane structure.