Background <p>The response and integration of cold signals are key processes when plants cope with cold stress. It remains a challenging problem to study the function of calcium (Ca²⁺) sensor in mediating the Ca²⁺ signaling during the early stage of cold signal transduction.</p> Results <p>Here, we focused on the Ca²⁺ sensor gene <i>OsCPK9</i> to explore its function in chilling tolerance. Our results showed that <i>OsCPK9</i> exhibits a significant cold-induced expression pattern, and contributes to chilling tolerance at seedling stages. The haplotype and population genetics analysis indicated that the promoter region of <i>OsCPK9</i> harbors favorable allelic variations that were strongly selected during the domestication process of <i>japonica</i> rice. Furthermore, OsCPK9 interact with five members of the OsSAPK family whose C-terminal domain is the determining factor. Upon exposure to chilling, OsCPK9 phosphorylates OsSAPK8 at Ser178 and Ser187, and stabilizes OsSAPK8 in a Ca²⁺-dependent manner, thereby activating the downstream responses.</p> Conclusions <p>Our findings demonstrated that the <i>OsCPK9</i>-<i>OsSAPK8</i> module regulates chilling tolerance through Ca²⁺-mediated phosphorylation during the early stages of cold signal transduction. Furthermore, the elite allelic variation of <i>OsCPK9</i> is an excellent candidate site for precise editing to enhance rice’s tolerance to chilling stress.</p>