Fluorescent bio-imaging has received significant attention in a myriad of research disciplines, and QDs are playing an increasingly important role in these areas. Doped QDs, an important alternative to conventional heavy metal-containing QDs are employed for biomedical applications. However, since QDs are exogenous substances to the biological environment, the biocompatibility of QDs is expected to be challenging in some cases. Herein, nano fluorine-doped hydroxyapatite (FAp, a well-known biocompatible material) was introduced to endow biocompatibility to Cd-free Mn-doped ZnSe@ZnS QDs. Thus, a nano-FAp-QD conjugate was developed and the biocompatibility, as well as potential cell imaging application, was investigated. To construct the proposed conjugate, Cd-free highly luminescent Mn-doped ZnSe@ZnS QDs and monodispersed nano-FAp were first prepared in high-temperature organic media. For facilitating the conjugation, hydrophobic nano-FAp was made water soluble via o-phosphoethanolamine (PEA) coating, which further provides conjugating sites for QDs to anchor. Cytotoxicity studies indicated the developed conjugate indeed possesses good compatibility and low toxicity to cells. The nano-FAp-QDs conjugate was successfully employed for cancer cell staining for at least 24 h, demonstrating the potential usefulness of this material in future biomedical research.