We report a preparation method for the synthesis of monodisperse magnetic polymer/silica hybrid microspheres using polymer microspheres incorporated with magnetic nanoparticles as a novel template. Monodisperse, hierarchically mesoporous, silica microspheres embedded with magnetic nanoparticles were successfully fabricated after the calcination of the hybrid microspheres. The magnetic nanoparticles were encapsulated in silica and distributed over the whole area of the porous microspheres without leakage. The resulting inorganic materials possess highly useful properties such as high magnetic nanoparticle loading, high surface area, and large pore volumes. The hierarchically mesoporous magnetic silica microspheres resulted in a high bovine serum albumin (BSA) protein adsorption capacity (260 mg/g) and a fast adsorption rate (reaching equilibrium with 8 h).