Ca²⁺ signals participate in various cellular processes with spatial and temporal dynamics, among which, inositol 1,4,5-trisphosphate receptors (IP₃Rs)-mediated Ca²⁺ signals are essential for early development. However, the underlying mechanisms of IP₃R-regulated cell fate decision remain largely unknown. Here we report that IP₃Rs are required for the hematopoietic and cardiac fate divergence of mouse embryonic stem cells (mESCs). Deletion of IP₃Rs (IP₃R-tKO) reduced Flk1⁺/PDGFRα⁻ hematopoietic mesoderm, c-Kit⁺/CD41⁺ hematopoietic progenitor cell population, and the colony-forming unit activity, but increased cardiac progenitor markers as well as cardiomyocytes. Concomitantly, the expression of a key regulator of hematopoiesis, Etv2, was reduced in IP₃R-tKO cells, which could be rescued by the activation of Ca²⁺ signals and calcineurin or overexpression of constitutively active form of NFATc3. Furthermore, IP₃R-tKO impaired specific targeting of Etv2 by NFATc3 via its evolutionarily conserved cis-element in differentiating ESCs. Importantly, the activation of Ca²⁺–calcineurin–NFAT pathway reversed the phenotype of IP₃R-tKO cells. These findings reveal an unrecognized governing role of IP₃Rs in hematopoietic and cardiac fate commitment via IP₃Rs–Ca²⁺–calcineurin–NFATc3–Etv2 pathway.