The pristine Fe3O4 nanoparticle (FeNP) is supposed to be a good catalyst of Fenton processes which have shown significant potential for water purification. Herein the magnetic macroporous hydrogel beads, having an open-cell structure, were synthesized by sedimentation polymerization of pristine FeNP stabilized oil-in-water high internal phase emulsions. The effects of the FeNP amount, internal phase fraction, and the costabilizer Tween85 concentration on the structure, such as interconnecting degree, void size, and its distribution of both the surface and inner of the beads, were investigated. With a methyl orange (MO) aqueous solution passing through a chromatography column that was filled with the FeNPs loaded hydrogel beads, the efficiency of these hydrogel beads as catalyst for Fenton reaction to decompose MO in water was tested. The MO was decomposed quickly at the first hour, followed by decomposed gradually in a further 5 h, and the decomposition rate of MO could be up to 99.6% at the end of the test. Moreover, MO decomposition rate remained over 98.2% in six batches which were run in the same beads filled column. The results showed that these FeNPs loaded porous hydrogel beads were reusable and highly efficient supporter for catalysis of Fenton reaction for decomposing organic pollutants in water.