Modification of catalysts by multi-heteroatom doping (S, P, B) is an effective way to improve the peroxomonosulfate activation performance of catalysts. In recent years, highly toxic and persistent trace organic contaminants have been frequently detected in water. Consequently, we proposed the advanced oxidation processes of peroxomonosulfate activated by multi-heteroatom doped Fe@CN (X-Fe@CN) to eliminate trace organic contaminants. The physical phases of X-Fe@CN and its precursors were characterized by X-ray diffraction and scanning electron microscopy. In evaluating the catalytic properties and iron ion leaching of X-Fe@CN-activated PMS for the removal of dicamba and atenolol, B-Fe@CN and PB-Fe@CN were selected and optimized. The active sites of the catalysts were characterized by X-ray photoelectron spectroscopy and Raman. The pathways of PMS activation by B-Fe@CN and PB-Fe@CN were identified in combination with electron paramagnetic resonance and electrochemical experiments. Defects, O-B-O and pyrrolic nitrogen on the surface of B-Fe@CN could adsorb and activate PMS to produce SO₄^•−, ·OH and ¹O₂. Further doping with P enhanced the electron transfer on the catalyst surface, thus accelerating the activation of peroxomonosulfate. This study compared the effects of multi-heteroatom modifications and further demonstrated the synergistic effect between P and B, which can provide a theoretical basis for the selection of multi-heteroatom doped catalysts in water treatment.