Magnesium ions (Mg 2+ ) are widely present in biological fluids, and they are suggested as the vital factors that inhibit spontaneous hydroxyapatite (HAP) precipitation in nature. However, the regulation mechanisms of Mg 2+ on HAP crystallization are still under intensive debates. We find that a typical precipitation of HAP from supersaturated solutions should include five stages: s1, formation of ion clusters and amorphous calcium phosphate (ACP); s2, stabilization of ACP; s3, transformation from ACP to HAP via dissolution and crystallization; s4, classical crystal growth of HAP; s5, HAP aging under a near equilibrium state. Actually, Mg 2+ ions exhibit different inhibitory effects on these stages. The ions have a negligible influence on the kinetics of initial ACP formation in solutions (s1) and final aging of crystals (s5). Rather, the ions can either adsorb onto or incorporate into the ACP precursor particles during s1. In s2, the lifetime of ACP in solution is extended significantly by both two types of Mg 2+ ions. However, the absorbed ones are more effective than the incorporated ones on the inhibition of the phase transformation from ACP to HAP in this s2. In stages of s3 and s4, it is only surface Mg 2+ ions that retard crystal growth of HAP and the incorporated Mg 2+ become inert. These detailed findings reveal how Mg 2+ ions affect the crystallization process of HAP mineralization from supersaturation. Such a detailed understanding can provide a chemical strategy for precise regulation of HAP formation kinetics in intermediate phase mediated crystallization.