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Salt is harmful to crop production. Therefore, it is important to understand the mechanism of salt tolerance in rice. <i>CIPK</i> genes have various functions, including regulating salt tolerance and other types of stress and nitrogen use efficiency. In rice, OsCIPK24 is known to regulate salt tolerance, but other OsCIPKs could also function in salt tolerance. In this study, we identified another OsCIPK—OsCIPK9—that can regulate salt tolerance. Knockout of <i>OsCIPK9</i> in rice could improve salt tolerance. Through expression analyses, <i>OsCIPK9</i> was found to be mainly expressed in the roots and less expressed in mature leaves. Meanwhile, <i>OsCIPK9</i> had the highest expression 6 h after salt treatment. In addition, we proved the interaction between OsCIPK9 and OsSOS3. The RNA-seq data showed that <i>OsCIPK9</i> strongly responded to salt treatment, and the transporters related to salt tolerance may be downstream genes of <i>OsCIPK9</i>. Finally, haplotype analyses revealed that Hap6 and Hap8 mainly exist in <i>indica</i>, potentially providing a higher salt tolerance. Overall, a negative regulator of salt tolerance, OsCIPK9, which interacted with OsSOS3 similarly to OsCIPK24 and influenced salt-related transporters, was identified, and editing <i>OsCIPK9</i> potentially could be helpful for breeding salt-tolerant rice.