Magnetic nanoparticles are frequently coated with SiO2 to improve their stability, biocompatibility and functionality for they become promising for many biomedical applications, such as MR imaging contrast agents, magnetically-targeted drug delivery vehicles, agents for hyperthermia, etc. In our study, we demonstrated a novel and time reducing modified sol-gel approach for obtaining a uniform Fe3O4/SiO2 core/shell nanocubes. Furthermore, the thickness of the silica shell is easily controlled in the range of 5-16 nm by adjusting the reaction parameters. The core/shell nanocubes samples were characterized by X-ray diffractometry (XRD), Transmission Electron Microscopy (TEM), Energy Dispersive Spectrometer (EDS), fourier transform infrared spectroscopy (FTIR), and vibrating sample magnetometer (VSM). The as-prepared Fe3O4/SiO2 core/shell nanocubes showed good stability in air for at least 4 month as well as against annealing condition of up to 300°C in presence of H2 gas as a strong reducing agent. Furthermore, high magnetization value of 50.7 emu/g was obtained for the sample with thin silica thickness (5 nm) as a consequence of shell thickness controlled. Moreover, the biocompatibility of the core/shell nanocube was enhanced in comparison to that of pristine Fe3O4 nanocubes. In addition, the Fe3O4/SiO2 nanocubes were functionalized by Aminopropy-ltriethoxysilane, and then conjugated with streptavidin-Cy3 successfully as indicated by fluorescence microscopy.