Superparamagnetic microspheres with an Fe₃O₄@SiO₂ core and a perpendicularly aligned mesoporous SiO₂ shell were synthesized through a surfactant-templating sol-gel approach. The microspheres possess high magnetization (53.3 emu/g), high surface area (365 m²/g), large pore volume (0.29 cm³/g), and uniform mesopore (2.3 nm). By using the unique core-shell microspheres with accessible large pores and excellent magnetic property, a fast removal of microcystins with high efficiency (>95%) can be achieved.