In this work, Mackinawite (FeSm) was synthesized by homogeneous precipitation method, and flower-like nanoparticles formed by the aggregation of nanosheets with a preferred orientation along the (001) plane. The heterogeneous Fenton-like degradation performance of FeSm on rhodamine B (RhB) was investigated, results illustrated that RhB degradation was the synergistic effect of adsorption, Fenton, and a heterogeneous Fenton-like reaction. In repeated experiments, the reduction of reactivity was attributed to the oxidation of FeSm into lepidocrocite, whereas lepidocrocite has relatively low hydroxyl radicals (•OH) production reactivity. Thus, it showed excellent degradation effects in long-time degradation of RhB. Photoluminescence technology and free radical capture experiments demonstrated that •OH produced on the surface of catalyst was the main active species to remove RhB. In addition, the Fe species on the surface of FeSm was the main active center for surface-mediated reactions. A total organic carbon test revealed that the degradation was not complete and degradation intermediates were formed. Liquid chromatography-mass spectrometry technology was used to identify the degradation intermediates. On this basis, possible degradation pathways were proposed.