Acute kidney injury (AKI) is characterized by a sudden decline in kidney function, often due to ischemia-reperfusion or nephrotoxic drugs. A key factor in AKI development is mitochondrial dysfunction, which disrupts energy and oxygen supply, increases ROS generation, and triggers inflammation. Addressing AKI through mitochondrial targeting remains challenging. Melatonin (MLT), a hormone secreted by the pineal gland, shows promise in AKI treatment. To enhance site-specific antioxidative efficacy, triphenylphosphonium-hyaluronic acid (TPP-HA), targeting CD44 receptors and mitochondria, was synthesized and linked to MLT via a cleavable linker, creating TPP-HA-TK-MLT (THTM). THTM improved MLT targeting in renal tubular epithelial cells through CD44 receptors and enhanced mitochondrial distribution via TPP. This effectively suppressed mitochondrial ROS under pathological conditions, ameliorated mitochondrial permeability and swelling, and increased resistance to stimuli such as ischemia-reperfusion injury or nephrotoxic drugs, reducing cell apoptosis. Moreover, THTM significantly reduced the progression of folic acid-induced kidney injury to chronic kidney disease, demonstrating its potential to lower the risk of chronic kidney disease.