Multimodal imaging using novel multifunctional nanoparticles provides a new approach for the biomedical field. Thiol-organosilica nanoparticles containing iron oxide magnetic nanoparticles (MNPs) as the core and rhodamine B in the thiol-organosilica layer (thiol OS-MNP/Rho) were synthesized in a one pot process. The thiol OS-MNP/Rho showed enhanced magnetic resonance imaging (MRI) contrast and high fluorescence intensity. The relaxometry of thiol OS-MNP/Rho revealed a novel coating effect of the organosilica layer to the MNPs. The organosilica layer shortened the T2 relaxation time but not the Tl relaxation time of the MNPs. We injected thiol-OS-MNP/Rho into normal mice intravenously. Injected mice revealed an alteration of the liver contrast in the MRI and a fluorescent pattern based on the liver histological structure at the level between macroscopic and microscopic fluorescent imaging (mesoscopic FI). In addition, the labeled macrophages were observed at the single cell level histologically. We demonstrated a new approach to evaluate the liver at the macroscopic, microscopic level as well as the mesoscopic level using multimodal imaging. (C) 2017 Elsevier Inc. All rights reserved.