To elucidate the molecular mechanisms of the MIX (combined in proportion to the content in Astragali Radix (AR), named the MIX) repairing podocyte damage to ameliorate nephropathy. MTT assay and western blot analysis were used to evaluate the protective effects of MIX on MPC5 cells induced by Adriamycin (ADR). Screening of potential pharmacodynamic markers, relevant drugs and disease targets were conducted by using metabolomics combined with bioinformatics, and the most relevant metabolic pathways were identified by analyzing shared target and KEGG pathways. The key mechanism was subsequently validated by cell adhesion assays, western blot assays, and immunofluorescence staining. The results showed that the MIX has the capacity to repair adriamycin-induced damage in MPC5 cells, as evidenced by enhanced cell viability and synaptopodin expression. Additionally, the MIX shows promise in potentially reinstating the podocyte adhesion through the modulation of the expression of podocyte adhesion-related proteins linked to nucleotide metabolites. The MIX has the potential to beneficially affect podocyte injury by modulating the cell adhesion pathway, contributing to one of the pharmacodynamic mechanisms of AR treatment of nephrotic syndrome. This has implications for the development and utilization of AR resources and achievement the social benefit of empowering rural revitalization.