Rhodium (Rh) nanoparticle (core)–carbon (shell) powder was prepared by double-layer coating of a silica layer and a mesoporous silica/carbon layer on an Rh nanoparticle followed by chemical etching with aqueous hydrofluoric acid to remove siliceous components. The use of various techniques for characterization of the structure showed that the powder thus-obtained had a rattle-like structure: Rh nanoparticles were encapsulated in the hollow carbon-shell having well-developed porosity. The porous wall structure of the lateral carbon shell provides channels and hydrophobic void spaces that allow efficient penetration and absorption of organic species present in aqueous media. This offers a microenvironment with a high concentration of organic substrates inside the shell. Moreover, the surfaces of medial Rh nanoparticles were free from any ligands, i.e., the active surface site(s) was exposed to induce organic transformations. These unique properties, which cannot be achieved by conventional Rh nanoparticles stabilized with organic agents, led to excellent catalytic activity for hydrogenation of various aromatic and heterocyclic rings in water.