Silica coated magnetite (Fe3O4@SiO2) core-shell nanoparticles (NPs) with controlled silica shell thicknesses were prepared by a modified Stöber method using 20 nm hydrophilic Fe3O4 NPs as seeds. The core-shell NPs were characterized by X-ray diffraction (XRD), transmission electron microscopy (TEM), high-resolution TEM (HRTEM), selected area electron diffraction (SAED), and UV-Vis adsorption spectra (UV-Vis). The results imply that NPs consist of a crystalline magnetite core and an amorphous silica shell. The silica shell thickness can be controlled from 12.5 nm to 45 nm by varying the experimental parameters. The reaction time, the ratio of TEOS/Fe3O4, and the concentration of hydrophilic Fe3O4 seeds were found to be very influential in the control of silica shell thickness. These well-dispersed core-shell Fe3O4@SiO2 NPs show superparamagnetic properties at room temperature.