The newly developed multifunctional (self-activated fluorescent, mesoporous, and biocompatible) hollow mesoporous silica nanoellipsoids (f-hMS) are potentially useful as a delivery system of drugs for therapeutics and imaging purposes. For the synthesis of f-hMS, self-activated fluorescence hydroxyapatite (fHA) was used as a core template. A mesoporous silica shell was obtained by silica formation and subsequent removal of the fHA core, which resulted in a hollow-cored f-hMS. Although the silica shell provided a highly mesoporous structure, enabling an effective loading of drug molecules, the fluorescent property of fHA was also well-preserved in the f-hMS. Cytochrome c and doxorubicin, used as a model protein and anticancer drug, respectively, were shown to be effectively loaded onto f-hMS and were then released in a sustainable and controllable manner. The f-hMS was effectively taken up by the cells and exhibited fluorescent labeling while preserving excellent cell viability. Overall, the f-hMS nanoreservoir may be useful as a multifunctional carrier system for drug delivery and cell imaging.