A novel surface modified anion exchange membrane (AEM) was prepared by electrodeposition of graphene oxide (GO) and polydopamine (PDA) coating, aiming at improving antifouling performance and stability. The AEM was firstly modified by electrodeposition of GO and then immersed into the dopamine solution to form a thin PDA layer. The effects of GO and PDA composite modification were investigated by various analytical techniques and electrodialysis application. The GO@PDA-modified AEM (GO@PDA-M) exhibited highly hydrophilic and negatively charged. In addition, the introduction of PDA coating helped to construct a smoother and denser composite modifying layer composed of GO and PDA, and reduced the roughness of membrane surface. Depending on these properties, the GO@PDA-modified AEM showed significant antifouling ability without compromising the desalination performance. After being fouled by 150 mg/L sodium dodecyl benzene sulfonate (SDBS) for 4 h, the desalination rate of GO@PDA-M increased by 39.3% compared to pristine membrane, while for PDA-modified membrane (PDA-M) and GO-modified membrane (GO-M) were 5.7% and 18.2% respectively. Moreover, it still maintained antifouling ability after 20 h of continuous operation. The stability of GO@PDA-M was immensely improved compared with the GO-M due to the introduction of PDA layer.