Magnetic/fluorescent (magnetofluorescent) materials have become one of the most important tools in the imaging modality in vivo using magnetic resonance imaging (MRI) and fluorescence imaging. We succeeded in fabricating magnetofluorescent nanoparticles (MFNPs) consisting of silicon/magnetite composite nanoparticles. Our unique synthetic approach can control simultaneously the magnetic and fluorescence behaviors by varying the particle size, demonstrating the superparamagnetic behavior and green fluorescence for the MFNPs having mean diameter of 3.0 nm, and the ferromagnetic behavior without fluorescence for the MFNPs having mean diameter more than 5.0 nm. More intriguingly, the MFNPs with superparamagnetism can detect green fluorescence even after the magnetic guidance of MFNPs by the commercial neodymium magnet. Additionally, the MFNPs having two magnetic behaviors also possess good biocompatibility.