A simple and flexible strategy based on droplet microfluidics is developed for controllable fabrication of uniform magnetic SiO₂ microparticles with highly-interconnected hierarchical porous structures for enhanced water decontamination. Uniform precursor water droplets containing surfactants and homogenized fine oil droplets with a relatively high volume ratio are generated from microfluidics as templates for microparticle synthesis via hydrolysis/condensation reaction. The SiO₂ microparticles possess hierarchical porous structures, containing both mesopores with size of several nanometers, and well-controlled and highly-interconnected macropores with size of hundreds of nanometers. The SiO₂ microparticles synergistically integrate fast mass transfer and large functional surface area for enhanced adsorption. To demonstrate the enhanced adsorption performances for organic dyes and toxic heavy metal ions, the microparticles are respectively used for removal of methylene blue in water, and modified with thiol-groups for removal of Pb²⁺ ions in water. Meanwhile, the microparticles can be easily recycled by magnetic field for reuse.