The biomineralization of CaCO₃ often involves the transformation of amorphous precursors into crystalline phases, which is regulated by various proteins and inorganic ions such as Mg²⁺ ions. While the effects of Mg²⁺ ions on the polymorph and shape of the crystalline CaCO₃ have been observed and studied, the interplay between Mg²⁺ ions and CaCO₃ during the mineralization remains unclear. This work focuses on the mechanism of Mg²⁺ ion-regulated mineralization of CaCO₃. By tracing the Mg isotope fractionation, the different mineralization pathways of CaCO₃ under different Mg²⁺ ion concentrations had been clarified. Detailed regulatory role of Mg²⁺ ions at the different stages of mineralization had been proposed through combining the fractionation data with the analyses of the CaCO₃ polymorph and shape evolution. These results provide a clear view of the Mg-mediated crystallization process of amorphous CaCO₃, which can be used to finely control the phase of the crystalline products according to different needs.