Uniform ruthenium nanoparticles (1–2 nm) confined in ordered mesoporous carbon (Ru-OMC) with various embedding degrees have been fabricated by using a boric acid-assisted hard template method. The catalytic performance of Ru-OMC catalysts was determined through the hydrogenation of toluene at 110 °C and 4.0 MPa. The effects of pore size and embedding degree on the catalytic performance were studied and compared with those of OMC-supported ruthenium (Ru/OMC) catalysts with various pore sizes. The catalytic activities of embedding Ru-OMC catalysts are much higher than those of supported Ru/OMC catalysts, which can be attributed to the strong interaction between ruthenium nanoparticles and the carbon support. Furthermore, the activities of Ru-OMC catalysts are closely related to the embedding degree of ruthenium nanoparticles in the carbon matrix. The Ru-OMC catalysts with an appropriate embedding degree affords a turnover frequency of up to 4.69 s−1 in toluene hydrogenation.