Astragali Radix (AR) has been used in the traditional Chinese medicine (TCM) in the treatment of various renal diseases for many years. In this study, a NMR based metabolomic approach coupled with biochemical assay and histopathological inspection had been employed to study the protective effect of total flavonoids (TFA) in AR against adriamycin-induced nephropathy using rats model. Multivariate analysis revealed that 11 of perturbed metabolites could be reversed by TFA, and the MetaboAnalyst analysis revealed that the anti-nephrotic syndrome effect of TFA was probably related with regulation of alanine, aspartate and glutamate metabolism, citrate cycle, pyruvate metabolism, cysteine and methionine metabolism and glyoxylate and dicarboxylate metabolism. The regulatory effects on the gene expression (ACE, nephrin, podocin) suggested that the anti-nephrotic syndrome effect of TFA was also related with the protection of renal filtration function and regulation of blood pressure. The system pharmacology analysis revealed 43 potential targets for TFA, and suggested that the protective effect of TFA on the nephrotic syndrome was probably related with the regulation of immune and renin-angiotensin system. These metabolic changes and the associated pathways, as well as the compound-target-disease network provide insights into the mechanisms of TFA for the treatment of nephrotic syndrome, and further studies are needed to validate the bioactive compounds responsible for the anti-nephrotic syndrome effect of TFA.