Magnetic resonance imaging (MRI) is an imaging modality adequate for in vivo studies. Therefore, many scientists are interested in the development of MRI probes capable of detecting enzyme activities in vivo. 19F MRI is useful for monitoring particular biosignals, cells, and target tissues, due to the absence of background signals in living organisms. Therefore, highly sensitive 19F MRI contrast agents are in great demand for their practical applications. However, we have faced the following challenges: (1) increasing the number of fluorine atoms decreases the solubility of the molecular probes, and (2) the restriction of the molecular mobility attenuates the 19F MRI signals. Herein, we developed novel multifunctional core–shell nanoparticles to solve these problems. They are composed of a core micelle filled with liquid perfluorocarbon and a robust silica shell. These core–shell nanoparticles have superior properties such as high sensitivity, surface-modifiability, biocompatibility, and sufficient in vivo stability. By the adequate surface modifications, gene expression in living cells and tumor tissue in living mice were successfully detected by 19F MRI.