The present invention relates to fullerene-silica nanoparticles with improved fluorescence, a preparation method of the fullerene-silica nanoparticles, and use thereof. More specifically, the present invention relates to fullerene-silica nanoparticles with improved fluorescence in which fullerene and silica are covalently linked, a preparation method of the fullerene-silica nanoparticles, and use thereof. The preparation method of the fullerene-silica nanoparticles comprises the steps of: adding a surfactant to a non-polar organic solvent and a polar solvent and stirring them to form reverse micelles (step 1); adding fullerene to the reverse micelles formed in the step 1 and stirring them (step 2); and adding a silica precursor and a catalyst to a reaction solution containing the fullerene prepared in the step 2 and stirring them to prepare fullerene-silica nanoparticles (step 3). According to the present invention, fullerene-silica nanoparticles in the form of a uniform spherical shape of tens of nanometers can be prepared. As such prepared fullerene-silica nanoparticles have a large surface area due to a nanometer-sized structure, they have good reactivity. Compared with heavy metals or metal nanoparticles, the fullerene-silica nanoparticles, because of using silica, are harmless to a living body. Further, as the fullerene-silica nanoparticles exhibit strong fluorescence, they can be used as a contrast agent for in-vivo imaging or as a drug delivery carrier.