Hydroxyapatite (HAp) is widely accepted as bone graft substitutes for clinical application. A novel method is to synthesize an applicable HAp nanoparticles which emit fluorescence or maintain magnetic property with quenching. The present invention is related to utilize CdSe/ZnS or magnetic nano particles as the nuclei for the growth of HAp crystal. The resulted HAp nanoparticles maintain the fluorescent or magnetic characteristics of CdSe QDs or magnetic nanoparticles and exhibit a shell structure of HAp which is recognized by the biological environment. The HAp nanoparticles emit fluorescence or maintain magnetic property which is useful for tracking and could find future clinical applications especially when employed as the tool for in vitro study of bone tissue engineering.