It is known that organic species regulate fabrication of hierarchical biological forms via solution methods. However, in this study, we observed that the presence of inorganic ions plays an important role in the formation and regulation of biological spherical hydroxyapatite formation. We present a mineralization method to prepare ion-doped hydroxyapatite spheres with a hierarchical structure that is free of organic surfactants and biological additives. Porous and hollow strontium-doped hydroxyapatite spheres were synthesized via controlling the concentration of strontium ions in a calcium and phosphate buffer solution. Similarly, fluoride and silicon-doped hydroxyapatite spheres were synthesized. While spherical particle formation was attainable at low and high temperature for Sr-doped hydroxyapatite, it was only possible at high temperature in the F/Si-doped system. The presence of inorganic ions not only plays an important role in the formation and regulation of biological spherical hydroxyapatite, but also could introduce pharmaceutical effects as a result of trace element release. Such ion release results showed a sustained release with pH responsive behavior, and significantly influenced the hydroxyapatite re-precipitation. These ion-doped hydroxyapatite spheres with hollow and porous structure could have promising applications as bone/tooth materials, drug delivery systems, and chromatography supports.