To avoid the dangerous operational conditions, shorten the preparation time, and improve the adsorption performance of amino-functionalized nanomagnetic materials with a core–shell structure, a magnetic nanocomposite of CoFe2O4@SiO2 was successfully functionalized with amino group (−NH2) through a mild and facile hydrothermal method without the use of any toxic or harmful solvents at a relatively low temperature. The preparation time of the key steps of amino functionalization was shortened from 30 h to about 10 h. The core-shell structure and successful grafting were confirmed by various means. The amino-functionalized CoFe2O4@SiO2 was used for the removal mercury (Hg(II)), a heavy metal, and exhibited excellent magnetic properties and a high Langmuir adsorption capacity of 149.3 mg Hg(II)/g. The adsorption of Hg(II) onto CoFe2O4@SiO2–NH2 followed the pseudo-second-order kinetic equation and Langmuir model. The thermodynamic data showed that the Hg(II) adsorption process was achieved through spontaneous exothermic and monolayer adsorption with electrostatic adsorption and chemisorption. In addition, the as-prepared CoFe2O4@SiO2–NH2 nanoparticles had a good reusable value, good application performance and stability, and can provide a mild and facile way to remove heavy metals from aqueous solution.