This study examined the purification of wastewater from the chemical mechanical polishing (CMP) process via a superconducting high gradient magnetic separation (HGMS) system. To remove silica, the main contaminant in CMP wastewater, the optimal coagulation process of silica-magnetite-ferric hydroxide aggregates was empirically determined. Filtration tests via superconducting HGMS system with optimal coagulation process were conducted with respect to the magnetic field and wastewater flow rate. The turbidity and Si concentration of the wastewater filtered at 2 T and 400 mL/min were in accordance with the grey water standard and reverse osmosis (RO) feed water requirement, which demonstrated the feasibility of the superconducting HGMS system for the purification of CMP wastewater.