In this paper, attempts have been made to prepare the nano-crystalline hydroxyapatite similar to the natural one. First, the pure hydroxyapatite solution was prepared via chemical sedimentation method. The pure hydroxyapatite was made in an aqueous media by adding calcium chloride (CaCl2) to phosphoric acid (H3PO4) with a molar ratio of Ca/P= 1.66 in the presence of 2M acetic acid (CH3COOH). Then by inserting carbonate agent (CO3-2) into the initial hydroxyapatite structure the carbon apatite was formed. This was done by adding different amounts of sodium carbonate (Na2CO3), and considering different molar rations CO3-2/PO4-3. Sodium-carbonated apatite was precipitated in an alkaline solution. FTIR and XRD systems were utilized to evaluate the present of the agent groups and the desired phases. The morphology and microstructure of the samples were studied using a TEM apparatus. The results confirm the formation of sodium-carbon apatite nano-crystal. These were also pointed out that the increasing the carbon in hydroxyapatite structure causes the reduction of the crystallinity degree, increases the solubility rate and changes the morphology of nano-crystals.