Synthesized hydroxyapatite (sHA)—calcium phosphate (CaP) based biomaterials play a vital role and have been widely used in the process of bone regeneration for bone defect repair, due to their similarities to the inorganic components of human bones. However, for bone tissue engineering purpose, the composite components, physical and biological properties, efficacy and safety of sHA still need further improvements. In this work, we synthesized inhomogeneous hydroxyapatite based on biomimetic trace elements (Mg, Fe, Zn, Mn, Cu, Ni, Mo, Sr, Co, BO₃³⁻, and CO₃²⁻) co-doped into HA (THA) (Ca_10−δM_δ(PO₄)_5.5(CO₃)_0.5(OH)₂, M = trace elements) via co-precipitation from an ionic solution. The physical properties, their bioactivities using in vitro osteoblast cells, and in vivo cytotoxicity using zebrafish were studied. By introducing biomimetic trace elements, the as-prepared THA samples showed nanorod (needle-like) structures, having a positively charged surface (6.49 meV), and showing paramagnetic behavior. The bioactivity studies demonstrated that the THA substrate can induce apatite particles to cover its surface and be in contact with surrounding simulated body fluid (SBF). In vitro biological assays revealed that the osteoblast-like UMR-106 cells were well-attached with growth and proliferation on the substrate’s surface. Upon differentiation, enhanced ALP (alkaline phosphatase) activity was observed for bone cells on the surface of the THA compared with that on the control substrates (sHA). The in vivo performance in embryonic zebrafish studies showed that the synthesized THA particles are nontoxic based on the measurements of essential parameters such as survivability, hatching rate, and the morphology of the embryo. The mechanism of the ions release profile using digital conductivity measurement revealed that sustained controlled release was successfully achieved. These preliminary results indicated that the synthesized THA could be a promising material for potential practical applications in bone tissue engineering.