In this paper, we report a novel synthesis and selective bioseparation of the composite of Fe3O4 magnetic nanocrystals and highly ordered MCM-41 type periodic mesoporous silica nanospheres. Monodisperse superparamagnetic Fe3O4 nanocrystals were synthesized by thermal decomposition of iron stearate in diol in an autoclave at low temperature. The synthesized nanocrystals were encapsulated in mesoporous silica nanospheres through the packing and self-assembly of composite nanocrystal–surfactant micelles and surfactant/silica complex. Different from previous studies, the produced magnetic silica nanospheres (MSNs) possess not only uniform nanosize (90 ∼ 140 nm) but also a highly ordered mesostructure. More importantly, the pore size and the saturation magnetization values can be controlled by using different alkyltrimethylammonium bromide surfactants and changing the amount of Fe3O4 magnetic nanocrystals encapsulated, respectively. Binary adsorption and desorption of proteins cytochrome c (cyt c) and bovine serum albumin (BSA) demonstrate that MSNs are an effective and highly selective adsorbent for proteins with different molecular sizes. Small particle size, high surface area, narrow pore size distribution, and straight pores of MSNs are responsible for the high selective adsorption capacity and fast adsorption rates. High magnetization values and superparamagnetic property of MSNs provide a convenient means to remove nanoparticles from solution and make the re-dispersion in solution quick following the withdrawal of an external magnetic field.