Heterogeneous peroxymonosulfate (PMS) activation is of great potential for sustainably degrading antibiotics included emerging contaminants from water. However, developing synthetic metal catalysts with incompatible mass transfer and optimized metal sites to effectively enable low-levels PMS activation and antibiotics removal is challenging. Herein, a protein-like Co catalyst of spatially hierarchical hydrophilicity is synthesized by constructing flower-like Mg/Al layered double hydroxide (LDH) on super-active carbon (AC) to disperse thin-layer Co(OH)2 along the edge of LDH. The resulting AC-LDH@Co(OH)2 catalyst demonstrates an impressive antibiotic removal of ≈80% within 15 s and turnover frequency of 45.72 min−1 based on catalyst mass by activating 0.075 mM PMS, surpassing single-atom catalysts included reports. In a fixed-bed reactor with secondary wastewater effluent, AC-LDH@Co(OH)2 realizes complete removal of norfloxacin for 66 h with neutral effluent pH and negligible metal leaching. Experiments combined with theoretical computations reveal that the protein-like complex not only accelerates transfer of low-levels hydrophilic PMS and hydrophobic antibiotics, but also stably confines Co sites with regulated electronic structure for multiply reactive oxygen species generation.