In clinical practice, sodium-glucose transporter 2 inhibitor (SGLT2i) reduces the composite renal outcomes in patients with diabetic kidney disease (DKD). However, its effect on regulating renal mitochondria remains unclear. Mitochondrial quality control (MQC) has been identified as a key factor in DKD. Peroxiredoxin3 (Prdx3) serves as a primary antioxidant protein in mitochondria. In this study, we investigated the expression of Prdx3 in patients with DKD, diabetic mice and HK-2 cells exposed to high glucose and explored SGLT2i potential mechanism of action. The results also showed that empagliflozin (Empa) treatment improved proteinuria and ameliorated renal pathological damage. We observed that Empa has an impact on the expression of Prdx3 in diabetic mice and HK-2 cells exposed to high glucose, so does the mitochondrial dynamic proteins and mitophagy-related proteins Mfn2, Drp1, PINK1, Parkin, LC3II, and P62. In vitro experiments after transfected with pcDNA3.1(+)-Prdx3 and siPrdx3 the expression of Mfn2, Drp1, PINK1, Parkin, LC3II, and P62 changed. The expression of PINK1 decreased after the knockdown of Prdx3. Furthermore, the knockdown of PINK1 accelerated the MQC damage and weakened the protective effect of Empa. Because Empa has impacts on Prdx3, which plays a protective role by influencing MQC, we investigated the latent impact of Prdx3 deficiency on renal injury and its molecular mechanism in vivo and in vitro in DKD. Herein, we demonstrate that Empa treatment modulates MQC potentially via Prdx3 through interacting with PINK1.