Owing to their many advantages including chemical inertness, low toxicity, and stable photoluminescence, carbon dots (CDs) have been considered as one of the rising fluorescent materials in the field of bio-labeling. Despite many burgeoning achievements in optical cell imaging, the exploration of multifunctional CDs for in vivo imaging and potential biotherapy is still a great challenge. In this work, carbon dots embedded in silica nanorattle (CDs@SN) nanocomposites exhibiting strong luminescence were prepared via a facile hydrothermal method. The structure and optical properties of the resultant CDs@SN were well studied by Fourier transform infrared (FT-IR) spectrum, transmission electron microscopy (TEM), and photoluminescence. The resultant CDs@SN was used for in vitro cell labeling and in vivo bioimaging, and exhibits a higher cellular uptake and brighter fluorescence than CDs alone. Furthermore, the CDs@SN shows excellent biocompatibility with HepG2 and red blood cells. We deem that combining the outstanding properties of SNs with CDs would further promote the development of CDs in biological applications, especially achieving multifunctional CDs with targeting, in vivo imaging and therapeutic-delivery capabilities.