Spinal cord injury (SCI) is a major public health challenge, often leading to severe neurological and physical disabilities. Microglia, the primary immune cells in the spinal cord, play critical roles in both the physiology and pathology of SCI. A deeper understanding of microglial activation is thus crucial for developing new therapeutic strategies. In this study, we observed that nicotinamide nucleotide transhydrogenase (NNT), a mitochondrial protein in eukaryotic cells, was upregulated in the injured spinal cord of mice, coinciding with elevated inflammatory factors and microglial activation. In vitro, lipopolysaccharide (LPS) induced microglial activation and increased NNT expression in BV2 cells. NNT overexpression effectively mitigated LPS-induced inflammation, proliferation, and oxidative stress in BV2 microglia. Furthermore, treatment with the mitochondria-targeting peptide SS-31 reduced mitochondrial superoxide levels. SS-31 also suppressed the inflammatory, proliferative, and oxidative stress responses caused by NNT deficiency in BV2 cells. Critically, in vivo overexpression of NNT in the spinal cord attenuated microglial activation and promoted functional recovery after SCI. Our findings reveal that NNT suppresses microglial activation by modulating mitochondrial oxidative stress, offering a promising therapeutic avenue for SCI.