This paper reports a novel way for the synthesis of a europium (Eu)-doped fluor-hydroxyapatite (FHA) nanostructure to control the luminescence of hydroxyapatite nanophosphor, particularly, by applying optimum fluorine concentrations, annealed temperatures and pH value. The Eu-doped FHA was made using the co-precipitation method followed by thermal annealing in air and reducing in a H atmosphere to control the visible light emission center of the nanophosphors. The intensities of the OH group decreased with the increasing fluorine concentrations. For the specimens annealed in air, the light emission center of the nanophosphor was 615 nm, which was emission from the Eu ion. However, when they were annealed in reduced gas (Ar + 5% H ), a 448 nm light emission center from the Eu ion of FHA was observed. The presence of fluorine in Eu-doped FHA resulted in a significant enhancement of nanophosphor luminescence, which has potential application in light emission and nanomedicine.