Nanocrystalline Zn-substituted calcium hydroxyapatite (HA) powder was synthesized by wet chemical method. Detailed characterization was carried out with both experimental techniques and numerical simulation method. X-ray diffraction (XRD) patterns show the calcium phosphate maintains as the apatite phase when the atomic ratio of Zn/(Zn+Ca) is less than 17% Zn in aqueous solutions. The calcium phosphate crystallinility decreases with the Zn concentration increase. The morphological changes with Zn substitution in HA were investigated by TEM. Lattice parameters of the apatitic samples were determined by XRD Rietveld refinement method. A computational study using ab initio generalized gradient approximation density functional theory was performed on Zn-substituted HA. Comparison of the experimental and computer simulation results provides our insights of Zn substitution in apatite structure.