In this work, we made a comparative study on the differences in the mechanism, stability and applicability of H2O2/Fe3O4 and PDS/Fe3O4 systems for Rhodamine B (RhB) degradation. The RhB degradation rate of H2O2/Fe3O4 system could reach 71.5% at 60 min, and its primary mechanism was regarded as the heterogeneous catalysis occurring on Fe3O4 surface. In this process, the newly formed Fe2O3 covered the active sites on Fe3O4 surface, hindering the continuous interaction between H2O2 and Fe3O4. Alternatively, the RhB degradation rate of PDS/Fe3O4 system could reach 98.5% at 60 min, and the homogeneous and heterogeneous catalysis were equally important. In this process, the formed S2O82‐ promoted the cycle of iron species to produce a lot of OH and SO4−, which significantly improved degradation performance. The RhB degradation pathway of two oxidation systems went through N-de-ethylation, chromophore cleavage, ring-opening and mineralization. After six cycles of degradation experiment, the RhB degradation rate of H2O2/Fe3O4 and PDS/Fe3O4 systems still reached 67.3% and 93.7%, and the corresponding mass loss of Fe3O4 catalyst was only 2.68% and 4.5%, respectively. Next, the alkaline environment greatly hindered the catalytic decomposition of H2O2 by Fe3O4, thus the H2O2/Fe3O4 system had a narrow pH application range (4.0–6.0), but PDS could be activated effectively by Fe3O4 catalyst in a wide pH range (4.0–10.0). In addition, the PDS/Fe3O4 system presented the stronger adaptability to actual water (including Cl‐, CO32-, HCO3-) and multi-pollutant degradation (including methylene blue, acid orange 7, tetracycline and bisphenol A) than the H2O2/Fe3O4 system. Finally, the two oxidation systems both effectively reduced the toxicity of pollutants and presented the exact cost.