The significant effects of transparent exopolymer particles (TEP) on membrane fouling have attracted the attention of several researchers. Finding an effective method for controlling membrane biofouling caused by TEP is essential for the long-term stable operation of membrane systems. The results of this experimental study show that the coupling process of magnetic ion exchange resin (MIEX)/Ultrafiltration (UF) can significantly mitigate membrane biofouling induced by TEP. Compared with the UF process, the irreversible growth rate of TEP on the membrane in the MIEX/UF process decreased by 75.9%, and the synergistic irreversible accumulation rate of TEP and bacteria decreased by 81.2%. The irreversible adhesion of bacteria to the membrane was significantly reduced, effectively inhibiting the formation of the primary level of biofilm and the development of biofouling. Further analysis showed that the MIEX inhibited the conversion of TEP precursors to TEP, and the quaternary ammonium salt functional groups on the surface of the MIEX sterilized bacteria and inhibited their proliferation in water. More importantly, because the interfacial forces between TEP/bacteria and MIEX were much higher than those between them and the UF membrane, the deposition of MIEX on the membrane surface not only prevented TEP and bacteria from reaching the membrane surface, but also removed the deposited TEP and bacteria from the membrane surface by hydraulic backwashing.