Novel mesoporous CTAB-functionalized magnetic microspheres with a core/shell structure (mesoporous Fe3O4@SiO2@CTAB–SiO2) was fabricated via a simple sol–gel method combined with selective etching strategy. The morphology, porosity, magnetic property, composition, and structure of mesoporous Fe3O4@SiO2@CTAB–SiO2 were characterized. Subsequently, the as-prepared composites were successfully applied to remove trace PFOS (500 ng L−1) from water at acidic conditions (pH = 3). The fabrication mechanism of mesoporous Fe3O4@SiO2@CTAB–SiO2 and the impact of various factors on the removal of trace PFOS from water were systematically studied. The recyclability of the as-prepared composites was tested for, five times, at the same conditions.