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Human bone mineral is different in composition from stoichiometric hydroxyapatite (Ca10(PO4)6(OH)2) in that it contains additional ions, of which CO3 2- is the most abundant species. Two macroporous carbonate-substituted hydroxyapatite (CHA) scaffolds were prepared by treating a macroporous CaCO3 column (porosity, 88%; pore and hole size, 160 and 71 μm), prepared in this study, hydrothermally at 120 °C in 1 M phosphate solutions of (NH4)2HPO4 and K2HPO4. Especially, it was found that the CaCO3 was transformed into CHA after hydrothermal treatment (HT) for 24 h irrespective of the type of phosphate solution. Under HT for 24 h, the crystallite size and crystal shape of CHA prepared in K2HPO4 solution (KCHA) and those of CHA prepared in (NH4)2HPO4 (NH4CHA) were quite different from each other. Moreover, NH4CHA contained 2.09 wt % A-type CO3 2- out of 6.05 wt % CO3 2-, but KCHA contained a small amount of A-type CO3 2- (0.08 wt % out of 8.24 wt % CO3 2-). The chemical formulas were Ca9.23(NH4)0.12(PO4)5.36(CO3)0.64(OH)0.54(CO3)0.34 for NH4CHA and Ca8.18K0.5(PO4)4.72(CO3)1.28(OH)0.1(CO3)0.02 for KCHA. Therefore, the properties, such as carbonate type and content, and crystal shape, of CHA are significantly affected by the type of phosphate solution.