In this study, the mechanochemical synthesis of substituted hydroxyapatite (HA) containing zinc and silicon ions having a chemical formula of Ca10−xZnx(PO4)6−x(SiO4)x(OH)2−x, where x = 0.2, 0.6, 1.0, 1.5, and 2.0, was carried out. The synthesized materials were characterized by powder X-ray diffraction, Fourier transform infrared spectroscopy, transmission electron microscopy, and inductively coupled plasma spectroscopy. We found that HA co-substituted with zinc and silicate formed up to x = 1.0. At higher concentrations of the substituents, the formation of large amounts of an amorphous phase was observed. The cytotoxicity and biocompatibility of the co-substituted HA was studied in vitro on Hek293 and MG-63 cell lines. The HA co-substituted with zinc and silicate demonstrated high biocompatibility; the lowest cytotoxicity was observed at x = 0.2. For this composition, good proliferation of MG-63 osteoblast-like cells and an increased solubility compared with that of HA were detected. These properties allow us to recommend the synthesized material for medical applications, namely, for the restoration of bone tissue and manufacture of biodegradable implants.