Diabetic nephropathy (DN), a common complication of diabetes mellitus, is the main cause of end-stage nephropathy, and thus developing novel strategies for reversing DN remains urgent. Astragaloside IV (AS-IV), a glycoside extracted from the Astragalus membranaceus (Fisch.) Bunge, is a widely used Traditional Chinese Medicine (TCM) in China and presents diverse pharmacological properties including the protective effect on DN. However, the rudimentary mechanism of AS-IV in remedying DN remains indeterminate. Currently, we systematically explore the pharmacological mechanism of action of AS-IV for treating DN. Firstly, AS-IV was evaluated by ADME assessment, and 26 targets were screened out through target prediction. Then, we decipher the protein-protein interaction (PPI), Gene Ontology (GO) enrichment analysis, disease and pathway network analysis to obtain the specific molecular biological process and pharmacological activity of AS-IV in the treatment of DN. Meanwhile, both in vivo and in vitro experiments confirmed that AS-IV has anti-oxidative stress, anti-inflammatory, anti-epithelial-mesenchymal transition (EMT) effects, and can inhibit the Wnt/β-catenin signaling pathway, ultimately ameliorating the renal injury caused by high glucose. Additionally, we also applied molecular docking and molecular dynamics simulation to predict the specific binding sites and binding capacity of AS-IV and related targets. Overall, the comprehensive system pharmacology method and experiment validations provide an accurate explanation for the molecular mechanism of AS-IV in the treatment of DN. Moreover, it is expected to provide a brand new strategy for exploring the effective components of TCM.Copyright © 2020 Elsevier Ltd. All rights reserved.