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Magnetic anion exchange (MIEX) has been increasingly concerned owing to its excellent performance for the removal of dissolved organic carbon in the treatment of drinking water. In this study, the ability of ultrafiltration (UF) membrane fouling control was analyzed by different combination processes of MIEX-UF. A single cycle and multi-cycle operations were conducted, and the separated and integrated processes of MIEX-UF were compared. Membrane filtration resistance, removal of organics, and morphologies of the membrane surface were analyzed. The results of the short-term operation did not show any obvious improvement in the membrane fouling control in the separated process (compared to UF alone); however, a marked improvement was obtained in the integrated process. The membrane filtration resistance analysis showed that the cake resistance (Rc) and pore blocking resistance (Rp) in the integrated process were only 52 and 24% of the values in the separated process. The multi-cycle operation demonstrated that the cumulative rate of hydraulically irreversible fouling was 0.0021 in the integrated process and was much lower than that in the separated process (0.0182). The mechanistic analysis shows that in the integrated process, a dynamic layer was formed on the membrane surface by the deposited MIEX beads, which markedly decreased the accumulation of the membrane foulants on the membrane surface and in the membrane pores.