Aging is strongly linked to mitochondrial dysfunction, which disrupts energy metabolism and tissue homeostasis. The salivary gland is an energy-dependent organ, and mitochondrial decline contributes to age-related atrophy and impaired secretion. In this study, we investigated whether spermidine can restore mitochondrial function in aging salivary glands. In aging accelerated klotho deficient mouse, spermidine supplementation improved glandular histology, restoring acinar organization and reducing atrophy. Transcriptomic profiling revealed that spermidine induced extensive transcriptional reprogramming, characterized by the upregulation of mitochondrial metabolic pathways and suppression of inflammatory signaling. qRT-PCR and Western blot analyses confirmed increased expression of PPARγ mediated mitochondrial membrane potential such as PGC-1α, NRF1/2, and OXPHOS complex subunits. Furthermore, spermidine elevated mitochondria oxygen consumption rate, including basal respiration, ATP production, maximal respiration, and spare respiratory capacity. These results demonstrated that spermidine improves mitochondria respiratory capacity through activation of the PPAR–PGC-1α–NRF regulatory axis and may serve as a potential therapeutic strategy for restoring mitochondrial homeostasis and preserving salivary gland function during aging.