Diabetic nephropathy (DN) is a common and complicated chronic kidney disease around the world. To elucidate and find effective therapies of DN is of vital importance. In this paper, we have discovered that Cyanidin-3-O-glucoside (C3G), which is one of the anthocyanins, could alleviate high glucose induced podocytes dysfunction. MTT, flow cytometry assay and western blot analysis showed that C3G could reverse the increase of cell apoptosis under high glucose treatment in MPC5 cells by up-regulation of Bcl2 and down-regulation of Bax and cleaved-caspase 3. Moreover, C3G improved the autophagy decrease that was induced by high glucose through regulating the expression level of LC3 II/LC3 I, Beclin1 and p62. In addition, C3G inhibited epithelial-mesenchymal transition (EMT) by increasing E-cadherin and reducing Vimentin. By further mechanisms study, we found C3G activated the SIRT1 and AMPK which were inhibited in high glucose condition. Silencing SIRT1 blocked the effect of C3G on regulating cell apoptosis, autophagy and EMT. In summary, our current findings suggest the protective effect of C3G against high glucose induced podocytes dysfunction is by improving autophagy and reducing apoptosis and EMT via activating SIRT1/AMPK pathway. It might be a new insight for the treatment of DN.