Abstract Background and Aims Renal ischemia reperfusion injury (IRI) is a leading and common cause of AKI, and delayed recovery of IRI contributes to chronic kidney disease and even end-stage kidney disease. However, there is no effective prevention and treatment for IRI-AKI. Calycosin (CAL), an isoflavonoid phytoestrogen isolated from Radix astragali, has various pharmacological activities. However, whether CAL has a protective effect on renal IRI and its mechanism remains elusive. In this study, we aim to explore the effect and mechanism of CAL on IRI-AKI through bioinformatics and experiments in vitro and in vivo models, so as to provide potential candidate drugs for early intervention treatment of IRI-AKI. Method (1) In the first part, mice were intragastrically given CAL daily for 7 d, and subjected to bilateral renal artery occlusion for 35 min followed by reperfusion 24 h to establish the renal IRI model. HE staining was used to evaluate the renal pathological injury, and the renal function including serum creatinine (SCr) and blood urea nitrogen (BUN), was also examined. Meanwhile, inflammatory factors were detected. In cell experiments, HK-2 cells pretreated with 8,16 and 32 μM CAL were subjected with hypoxia/reoxygenation (H/R), and the effect of CAL on H/R induced cell injury were investigated by qRT-PCR and ELISA. (2) In the second part, the differentially expressed gene (DEGs) of IRI-AKI were obtained by bioinformatics analysis of GSE52004 dataset. Subsequently, the hub gene with the highest score was obtained by protein-protein interaction (PPI) analysis, and its upstream transcription factors were predicted by JASPAR database. In IRI-AKI mice, the predicted results of bioinformatics were verified by qRT-PCR, Western Blot and immunohistochemistry. In HK-2 cells, the regulatory relationship between the hub gene and its upstream transcription factor and the role of them in inflammatory process were verified by double luciferase reporter gene and siRNA. Furthermore, molecular docking was used to predict the interaction between CAL and the transcription factor, and the role of the target protein in the protection of H/R HK-2 cells by calycosin was verified by siRNA. Results (1) In the mice with renal IRI, CAL dose dependently alleviated SCr and BUN levels and renal tubular injury score. Meanwhile, the mRNA levels and concentrations of inflammatory cytokines were markedly inhibited by CAL pretreatment. (2) In the pre-experiment in vitro, the toxicity of CAL was negligible at concentrations of 32 μM or less for 24 h incubation. In H/R induced HK-2 cells, CAL incubation reduced the levels of hypoxia-inducible factor 1α (HIF-1α) and the inflammatory cytokines. (3) 58 DEGs were identified in the kidney of IRI mice. PPI analysis showed early growth response 1 (EGR1) is the hub gene the highest score. JASPAR database predicted that peroxisome proliferator-activated receptor γ (PPARγ) is the upstream transcription factor of EGR1. (4) In kidney after IRI, EGR1 was up-regulated and PPARγ was down-regulated, while the pretreatment of CAL decreased EGR1 and increased PPARγ in a dose-dependent manner. (5) In H/R induced HK-2 cells, after inhibited the expression of EGR1 by siRNA, the level of inflammatory factors decreased significantly, suggesting that EGR1 participated in and promoted the inflammatory process of tubular cells. In addition, dual luciferase reporter gene assay confirmed that PPARγ interact with EGR1 promoter, as EGR1 increased after EGR1 promoter plasmid transfection but decreased after PPARγ overexpression. (6) In mice after renal IRI, CAL promote PPARγ expression markedly. According to molecular docking, CAL, as a ligand, could be embedded into the orthosteric pocket of PPARγ with a binding energy of -6.46 kcal/mol. In CAL incubated cells, PPARγ increased and EGR1 decreased considerably. However, the protective effect of CAL on H/R induced inflammation was absent when PPARγ knockdown, indicated that CAL ameliorate renal IRI and inhibit inflammation via PPARγ/EGR1. Conclusion CAL could significantly modulate inflammation by targeting the PPARγ/EGR1 pathway, contributing to the alleviation of renal IRI.