In this study, novel Fe/C granules (FeCGs) were successfully prepared at room temperature by embedding iron filings and hydrothermal carbonization biochar in sodium alginate. The removal rate of ibuprofen (IBU) by the composite system of sodium persulfate and FeCG was 96.81%, and the removal rate of total organic carbon was 68.41% near neutral pH. The core-shell structure was stable and almost unchanged after use. Eight intermediates were detected in the degradation process, from which the degradation pathway of IBU was proposed. The results of the reusability and stability test showed that the removal rate of IBU was stable under the condition of poor water mobility. This study provides an alternative method to the treatment of contaminants in drugs and personal care products. The main finding of the work is to develop a novel core-shell structure FeCG and predict the pathway for IBU removal by FeCG reacting with peroxydisulfate.