A novel magnetic composite catalyst of MnOx loaded on MIL-100(Fe) was prepared for the removal of Hg0 from flue gas, via incipient wetness impregnation followed with calcination at 300 °C. The MIL-100(Fe) supported catalyst showed greater capacity of Hg0 adsorption and oxidation than Fe2O3 supported catalyst at all test temperatures, showing Hg0 removal efficiency of 77.4% at 250 °C with high GHSV of 18,000 h−1. Besides the merit of high BET surface area and developed porous, the ultra-highly dispersed and homogeneous Fe sites on MIL(Fe) significantly promoted Hg0 adsorption and oxidation via the synergy effect with MnOx. Furthermore, the catalyst exhibited magnetic property, which allowed easy separation of the catalyst from fly ash with a recovery of 104%. SO2, H2O and NH3 in flue gas were proved inhibited Hg0 removal via different mechanisms. SO2 and H2O competed and desorbed Hg2+ on the surface of catalyst, while NH3 was more likely to compete adsorption sites with Hg0.