Acute liver failure is a severe condition with high mortality, requiring effective treatments. Jiedu Huayu Granule, a traditional Chinese medicine, shows protective effects, but its molecular mechanisms remain unclear. This study aims to investigate the therapeutic mechanisms of Jiedu Huayu Granule in acute liver failure using integrated transcriptomic and proteomic analyses. Results: Transcriptomic and proteomic profiling of rat models identified three key genes (Fth1, Necap2, and Prdx2) whose expression was upregulated in acute liver failure and subsequently downregulated by Jiedu Huayu Granule treatment. Animal and cellular experiments confirmed these expression changes. Bioinformatics analysis linked these genes to crucial pathways including ribosome function, chemokine signaling, and fatty acid metabolism. Molecular docking predicted stable binding interactions between active components of the herbal formula and the proteins encoded by these key genes. Conclusion: Jiedu Huayu Granule may exert its therapeutic effects against acute liver failure by modulating the expression of Fth1, Necap2, and Prdx2 and their associated pathways. These findings provide a molecular basis for the clinical application of Jiedu Huayu Granule and suggest novel potential targets for acute liver failure treatment.