Novel complex nanospheres with core/shell structure for selective adsorption of Hg2+ have been prepared by a simple one-pot method. Scanning electron microscopy (SEM) and transmission electron microscope (TEM) images showed the nanospheres had perpendicularly thiol-functionalized mesoporous SiO2 hybrid shell and Fe3O4@SiO2 core (Fe3O4@nSiO2@mSiO2–SH). XRD patterns of as-synthesized nanospheres confirmed the observation of the SEM and TEM. The size of the nanospheres is about 100 nm. Based on the analysis of N2 sorption–desorption isotherm, the surface area and pore volume of the adsorbent are 861 m2/g and 0.48 cm3/g, respectively. The saturation magnetization value for Fe3O4@nSiO2@mSiO2–SH is as high as 6.87 emu g−1. The nanospheres showed more accessible active sites and high dispersibility in water, exhibited excellent performance for selective Hg2+ adsorption, had a stable structure, and could be recycled easily with magnet.