The regulation of leaf senescence and disease resistance plays a crucial role in determining rice grain yield and quality, which are important to meet the ever-increasing food demands of the world. Here, we identified an atypical Dof transcriptional factor OsDes1 that contributes to the stay-green phenotype, grain yield, and disease resistance in rice. The expression level of OsDes1 is positively associated with stay-green in natural variations of japonica rice, suggesting that OsDes1 would be alternatively used in breeding programs. Mechanistically, OsDes1 targets the promoter of the Rieske FeS protein gene OsPetC to activate its expression and interacts with OsPetC to protect against its degradation, thus promoting stay-green and ultimately improving the grain yield. OsDes1 also binds to the promoter region of defense-related genes, such as OsPR1b, and activates their expression, leading to enhanced disease resistance. These findings offer a potential strategy for breeding rice to enhance grain yield and disease resistance.