Oxidative stress is an important pathological mechanism for acute kidney injury (AKI). SS-31, as a mitochondria-targeted peptide with strong antioxidant activity, is a good candidate for the treatment of AKI. However, an efficient treatment of AKI requires frequent administration of SS-31, which is due to its poor specific biodistribution and low delivery efficiency. To overcome these deficiencies, we designed pH-responsive and AKI-kidney targeted nanopolyplexes (NPs) for effectively delivering SS-31, which is new frontier for formulation of HA and CS. NPs are electrostatically complexed using anionic hyaluronic acid and cationic chitosan as materials, which could increase the accumulation in injured areas and uptake into CD44-overexpressed cells. Electrostatic balance of NPs is broken in low pH environment of lysosomes to allow SS-31 releasing and subsequently targeting to mitochondria to represent therapeutic effect. In vitro studies indicate that NPs exhibited higher antioxidative and antiapoptotic effects as compared with free SS-31. AKI mouse model suggests that NPs have significantly higher therapeutic efficiency than bare SS-31. It was found that NPs had excellent ability to decrease oxidative stress, protect mitochondrial structure, reduce inflammatory response, reduce apoptosis and necrosis of tubular cells after intravenious administration. Overall, the results suggest that the NPs have significant potential to enhance the specific biodistribution and delivery of SS-31, therefore have good effects on reducing oxidative stress and inflammation, preventing tubular apoptosis and necrosis. We believe NPs are effective delivery system for AKI treatment in clinical application.