Lipid metabolism disorder and disturbed mitochondrial bioenergetics play pivotal roles in the occurrence and development of diabetic kidney disease (DKD). Berberine (BBR) is a kind of alkaloid derived from Chinese herbal medicine. It has multiple therapeutic actions on diabetes mellitus and its complications, including regulation of glucose and lipid metabolism, improvement of insulin sensitivity and alleviation of oxidative damage. Here we investigated the renoprotective effects of BBR.Combined clinical study in DKD patients with experimental studies in diabetic mice and cultured podocytes, we characterized the energy metabolism profiles based on metabolomics, investigated molecular targets and mechanisms of BBR at regulating mitochondrial function and bioenergetics, and testified the effects of BBR on metabolic alterations in DKD animal model.Metabolomics examination suggested altered mitochondrial fuel usage and generalized mitochondrial dysfunction in DKD patients. BBR intervention potently reversed metabolic disorders, podocyte damage and glomerulosclerosis in db/db mice. Lipid accumulation, excessive generation of mitochondrial reactive oxygen species, mitochondrial dysfunction and insufficient fatty acids oxidation in DKD mouse models and cultured podocytes were significantly suppressed by BBR. The protective mechanism of BBR might involve the activation of peroxisome proliferator-activated receptor γ coactivator-1α (PGC-1α) signaling pathway, thereby promoting mitochondrial energy homeostasis and fatty acid oxidation in podocytes.Our research elucidated that PGC-1α-mediated mitochondrial bioenergetics might play a key role in lipid disorder-induced podocyte damage and development of DKD. Restoration of PGC-1α activity and the energy homeostasis by BBR might be a potential therapeutic strategy against DKD.