Zn-substituted hydroxyapatite (ZnHA) has been studied as a biomaterial with enhanced biological activity, which is related to its crystal structure and micromorphology. We investigated the inner contacts at the sites of Zn-substitution, crystal structure conversion behavior and variation of morphology in ZnHA. The composition of samples with different Zn/(Zn+Ca) molar ratios (0 mol%, 1 mol%, 5 mol%, 10 mol% and 20 mol%) was characterized by means of X-ray diffraction (XRD) and Fourier-transform infrared spectroscopy (FTIR). The morphologies of samples were examined with scanning electron microscopy (SEM) and high-resolution transmission electron microscopy (HRTEM). The Zn2+ ion distribution was analyzed by means of X-ray photoelectron spectroscopy (XPS). From the XRD and FTIR data, it could be observed that the crystallinity of the precipitates decreased with increasing content of Zn2+ ions, with the formation of amorphous phase when the concentration of Zn2+ ions exceeded 10 mol%. SEM and HRTEM results showed that the morphologies changed from nano-needle clusters to nanospheres with increasing concentration of Zn2+ ions. According to the XPS results, at low Zn concentrations (0-5mol% Zn), the Zn2+ ions only occupied the Ca(II) sites. However, with the increase in the concentration of Zn2+ ions, Zn2+ ions also gradually occupied the Ca(I) sites. Hence, we can conclude that the change in morphology and crystal structure is affected by the Zn2+ ions occupying the different Ca2+ ions sites.