Zinc ions (Zn2+) have long been considered to inhibit calcium phosphate mineralization. However, most mechanistic studies employ supraphysiological concentrations, leaving its biological effects at physiologically low concentrations remain elusive. Here, the regulation mechanism of Zn2+ on amorphous calcium phosphate (ACP) crystallization kinetics was systematically investigated under physiological conditions using a series of advanced analytical and spectroscopic methods. Results showed that, at low concentrations, Zn2+ promoted the formation of smaller ACP precursors via enhancing liquid-liquid phase separation, compromising kinetic stability and accelerating phase transformation. In contrast, higher Zn2+ concentrations inhibited the nucleation and subsequent growth of hydroxyapatite (HAP) crystals. The overall crystallization kinetics were thus regulated by the competition between particle size-driven promotion and foreign ion-mediated inhibition, which effectively governed the overall transformation pathway. Furthermore, most Zn2+ was expelled from Zn-enriched ACP domains during HAP maturation, yet a small fraction of Zn2+ remained incorporated into the HAP crystal lattice, leading to a decreased crystallinity degree. Given the enhanced bioactivity of low-crystallinity HAP for bone repair, Zn-doped HAP represents a promising bone graft material. This work clarifies Zn2+ regulatory mechanisms in biomineralization, informing rational design of superior bone grafts.