The present invention relates to a perfluorocarbon nanoemulsion containing quantum dot nanoparticles and a method for preparing the same, more specifically, relates to a method for preparing a multifunctional perfluorocarbon nanoemulsion which simultaneously shows the fluorine-based magnetic resonance properties of perfluorocarbon and the optical properties of quantum dot nanoparticles, the method comprising dispersing quantum dot nanoparticles, modified with a fluorine end group, in perfluorocarbon, and then adding an aqueous emulsifier solution containing lipid to the dispersion. The disclosed perfluorocarbon nanoemulsion containing quantum dot nanoparticles has excellent biocompatibility and simultaneously shows optical properties and magnetic resonance properties, and thus can be used as a contrast agent for multi-mode molecular imaging. Accordingly, the nanoemulsion can be used to study cell and small-animal molecular imaging in various fields, including biological and medical fields.