Acute kidney injury (AKI) is often secondary to sepsis. Increasing evidence suggests that mitochondrial dysfunction contributes to the pathological process of AKI. In this study, we aimed to examine the regulatory roles of Sirt3 in Lipopolysaccharide (LPS)-induced mitochondrial damage in renal tubular epithelial cells (TECs). Sirt3 knockout mice were intraperitoneally injected with LPS, and cultured TECs were stimulated with LPS to evaluate the effects of Sirt3 on mitochondrial structure and function in TECs. Electron microscopy was used to assess mitochondrial morphology. Immunofluorescence staining was performed to detect protein expression and examine mitochondrial morphology. Western blotting was used to quantify protein expression. We observed that LPS increased apoptosis, induced disturbances in mitochondrial function and dynamics, and downregulated Sirt3 expression in a sepsis-induced AKI mouse model and human proximal tubular (HK-2) cells in vitro. Sirt3 deficiency further exacerbated LPS-induced renal pathological damage, apoptosis and disturbances in mitochondrial function and dynamics. On the contrary, Sirt3 overexpression in HK-2 cells alleviated these lesions. Functional studies revealed that Sirt3 overexpression alleviated LPS-induced mitochondrial damage and apoptosis in TECs by promoting OPA1-mediated mitochondrial fusion through the deacetylation of i-AAA protease (YME1L1), an upstream regulatory molecule of OPA1. Our study has identified Sirt3 as a vital factor that protects against LPS-induced mitochondrial damage and apoptosis in TECs via the YME1L1-OPA1 signaling pathway.