Sepsis-associated encephalopathy (SAE) is a common and serious complication of sepsis, characterized by neuroinflammation and cognitive dysfunction, yet its molecular mechanisms remain unclear. This study aimed to investigate the role of heat shock protein 90α (HSP90α) in microglial NLRP3 inflammasome activation and cognitive impairment in SAE, and to explore the therapeutic potential of a small molecule compound, nicotinamide N-oxide (NAMO). SAE models were established using cecal ligation and puncture (CLP) in mice and LPS/ATP stimulated primary microglial cells/BV-2 cells. A combination of H&E/Nissl/TUNEL staining, transcriptomics, immunoblotting, qPCR, immunofluorescence, ELISA, mtDNA release, co-immunoprecipitation, molecular docking, AAV stereotaxic delivery, and pharmacological/siRNA interventions were utilized. Results showed that HSP90α expression was significantly upregulated in microglia during SAE. HSP90α facilitated NLRP3 inflammasome activation and exacerbated cognitive dysfunction in SAE by inducing mitochondrial dysfunction and promoting the release of mitochondrial DNA (mtDNA). Mechanistically, HSP90α interacted with PPP3CA, which facilitated Drp1 dephosphorylation at Ser637, triggering mitochondrial fragmentation and mtDNA release. Importantly, we identified that NAMO binds directly to HSP90α, inhibits the HSP90α-PPP3CA-Drp1 axis, reduces mtDNA release, and suppresses NLRP3 inflammasome activation. Administration of NAMO significantly alleviated cognitive impairment in SAE mice. Collectively, our findings reveal a novel HSP90α-PPP3CA-Drp1-mtDNA-NLRP3 signaling pathway in microglial activation and cognitive injury during SAE, and propose NAMO as a promising therapeutic candidate for SAE intervention.