Fe3O4@SiO2 core-shell structured nanoparticles are promising candidates for adsorption of heavy metal ions from waste water due to their high adsorption capacities and feasible recycling process. However, their practical applications have been hindered by the trade-off between the magnetic separation efficiency and durability. In this study, we demonstrate the preparation of amino-functionalized Fe3O4@SiO2 absorbents with both high magnetic separation efficiencies and durability in strong acidic environment. Our key strategy was to use a thin but highly protective silica layer by manipulating the sol-gel chemistry. With the protection of a thin but poorly permeable silica shell, the durability of the Fe3O4 in strong acid solution was significantly enhanced while its magnetic separation efficiency was maintained. We also demonstrated the adsorption of Cu2+ from aqueous solution corresponded well with the pseudo-second-order kinetic model and the Langmuir adsorption isotherm. The adsorption capacity can be further improved by coating an additional layer of mesoporous SiO2 outside Fe3O4@SiO2. The design of highly durable magnetic absorbents without sacrificing the magnetic separation efficiency greatly facilitates the practical applications of magnetic nanoparticles in adsorption of heavy metal ions.