We successfully synthesized organic acid (citric acid (Cit), tris(hydroxymethyl)aminomethane (Tris))-coordinated Eu 3+ and F − co-doped hydroxyapatite (HA) particles, and control of the photoluminescence (PL) characteristics were evaluated and discussed. Specifically, F − and Cit ions suppressed the nonradiative deactivation of the Eu 3+ ion doped HA (Eu:HA) particles, achieving higher η int (33.7%) of red color emission. The carbon compounds, which emitted the blue color PL at 400−540 nm, were precipitated on the particles by the thermochemical changes at 180 °C in the Cit ions. When the thermochemical changes occurred under the coaddition of Cit with Tris, nitrogen-containing carbon compounds emitting blue color PL were precipitated, and the maximum PL wavelength was red-shifted with increasing thermal treatment time, which enhanced the green color emission. It was found that the chroma of the three primary colors can be effectively controlled by the PL intensity ratio of the carbon compounds to that of the Eu 3+ ions. As a result, we successfully synthesized HA particles emitting red, blue, and white color PL with higher chroma. The findings obtained in this study can contribute to the elucidation of the mechanism for effectively controlling the PL properties of Eu:HA particles by thermochemical changes of organic acid ions. Since the particles emitted PL color with higher chroma, the cell-labeling particles (i.e., bioimaging materials) can be easily distinguished from the self-luminous living tissues with the naked eye for direct detection.