Endosperm as the storage organ of starch and protein in cereal crops largely determines grain yield and quality. Despite the fact that several pentatricopeptide repeat (PPR) proteins required for endosperm development have been identified in rice, the molecular mechanisms of many P-type PPR proteins in endosperm development remains unclear. Here, we isolated a rice floury endosperm mutant ppr5 that developed small starch grains and an abnormal aleurone layer, accompanied by decreased starch, protein, and amylose contents. Map-based cloning combined with a complementation test demonstrated that PPR5 encodes a P-type PPR protein that is localized to the mitochondria. The mutation in PPR5 caused reduced splicing efficiency of mitochondrial NADH dehydrogenase 4 (nad4) gene intron 3 and reduced complex Ⅰ assembly and activity. Loss of PPR5 function greatly up-regulated expression of alternative oxidases (AOXs), reduced ATP production, and affected mitochondrial morphology. We demonstrate that PPR5, as a P-type PPR protein, is required for mitochondrial function and endosperm development by controlling the cis-splicing of mitochondrial nad4 intron 3.