Hydroxyapatite (HA) particle, which is an inorganic component of biological hard tissues, is being applied as a bioceramic for biotechnology and medicine fields. However, early bone formation is difficult in the implantation of well-known stoichiometric HA into our body. To solve this problem, it is important to control the shapes and chemical compositions of the physicochemical properties of HA to be functionalized as the state similar to the biogenic bone. In this study, the physicochemical properties of the HA particles synthesized in the presence of tetraethoxysilane (TEOS) (SiHA particles) were evaluated and investigated. In particular, the surface layers of the SiHA particles were successfully controlled by adding silicate and carbonate ions in the synthetic, which would be involved in the bone formation process, and their elusive reaction behavior with phosphate-buffered saline (PBS) was also evaluated. The results showed that the ions in the SiHA particles increased with the increase in the added TEOS concentration, and the silica oligomer was also formed on the surfaces. The ions were present not only in the HA structures but also on the surface layers, indicating the formation of the non-apatitic layer containing the hydrated phosphate and calcium ions. The change in state of the particles with the immersion in PBS was evaluated, the carbonate ions eluted from the surface layer into PBS, and the free water component in the hydration layer increased with the immersion time in PBS. Therefore, we successfully synthesized the HA particles containing silicate and carbonate ions, suggesting the important state of the surface layer consisting of the characteristic non-apatitic layers. It was found that the ions in the surface layers can react with PBS and leach out, weakening the interaction of hydrated water molecules on the particle surfaces to increase the free water component in the surface layer.