Schiff-base functionalized superparamagnetic Fe3O4 composites (Fe3O4@SiO2-HO-S and Fe3O4@SiO2-HE-S) were synthesized by homogeneous and heterogeneous method, respectively. Their structures were characterized by FTIR, elemental analysis, SEM, TEM, TGA, XRD, and porous structure analysis. The feasibility of Fe3O4@SiO2HO-S and Fe3O4@SiO2-HE-S for the removal of Pb(II) and Cd(II) from aqueous solution was systematically investigated. The effects of pH, time, temperature, and initial metal ions concentration on the adsorption were determined. Results demonstrated that the optimal adsorption pH for both Pb(II) and Cd(II) is 6. Adsorption kinetic showed that the adsorption equilibrium time for Pb(II) and Cd(II) are 270 and 210 min, respectively. Adsorption kinetic followed pseudo-second order model and dominated by film diffusion process. Isotherm adsorption indicated that the adsorption capacity increased with the increase of metal ion concentration and temperature. The isotherm adsorption process can be well depicted by Langmuir isotherm model. Thermodynamic parameters indicated that the adsorption process is spontaneous, endothermic, and randomness- increasing process. FTIR and DFT calculation demonstrated the interaction between N atom and metal ion dominated the adsorption of Pb(II) and Cd(II), while O atom also participated in the coordination. Charge transfer occurred from Schiff base ligand to Pb(II) and Cd(II) during the adsorption process.