Nano-meter scale Ca-deficient hydroxyapatite (nano-apatite) is a potential candidate as artificial bone substitute materials owing to its similarity to the bone with respect to composition, morphology and osteoclastic degradation or adsorbent materials for blood purification therapy to remove pathogenic substances. The initial biodegradation behaviors, the initial cell-material interaction and the protein adsorption properties of nano-apatite must depend on the microstructure. The purpose of this study is the preparation of nano-apatite particles and their structural characterization by using X-ray diffraction (XRD) and solid-state NMR spectroscopy. The nano-apatite particles were prepared by precipitation processing method, and the effects of magnesium ions on the precipitation of calcium phosphate were examined, because Mg ions are well-known to play a role of inhibition of crystal growth. The addition of Mg ions led to the precipitation of nano-meter scale Ca-deficient apatite crystals having 1.33-1.63 of the molar ratio (Mg+Ca)/P. NMR analyses showed that the microstructure of Mg•HAp particles can be explained by a crystalline HAp core covered with a thin amorphous hydrated calcium phosphate layer.