We synthesized citric acid (Cit)-coordinated Eu3+ and F– codoped hydroxyapatite (Cit/Eu:HA-F) nanoparticles (NPs) and investigated their ion diffusion processes based on photoluminescence (PL) properties at the near-surfaces with thermal treatment. At 85 °C, the Cit coordination layer effectively suppressed the nonradiative deactivation of HA NP surfaces in the PL process, and the quantum yield (ηint) of Eu3+ ions reached a maximum value of ca. 33%, indicating the highest PL efficiency in the HA system. At 250 °C, Cit was decomposed into aconitic acid with a high optical absorption coefficient and reducing ability, so that the ηint of the Eu ions in the NPs were minimized and the partial Eu3+ ions were resultantly reduced to Eu2+ ions. At around 350 °C, the Eu ions were partially diffused from Ca(I) into Ca(II) sites. At 550 °C, the proportion of Eu ions in Ca(II) sites dramatically reached up to ca. 31%, and the F– ions simultaneously diffused into the HA structures by substituting for the OH sites. Therefore, it was elucidated that the Cit molecules coordinated to the Eu and F– codoped HA surfaces achieved higher ηint and promoted the diffusion of various ions into the HA structures with thermal treatment and resultantly controlled the existence ratio of the Eu3+ and Eu2+ ions at the near surfaces, which could be expected to control the PL color by the Cit coordinative mediation technique and realize the creation of cell-labeling luminescent nanomaterials in biomedical fields.