Many herbs and herbal formulae have been proven to offer safe and effective treatment for hyperlipidemia. However, the molecular mechanisms of their treatment have not been fully elucidated. Here, a total of 103 herbal formulae, including 146 individual herbs used to treat hyperlipidemia, were screened. Next, 40 common targets of core herbs and hyperlipidemia were extracted, representing potential targets of the herbal medicines for the treatment of hyperlipidemia. Further analysis revealed that the seven proteins most relevant to hyperlipidemia treatment were IL6, AKT1, IL1B, PTGS2, VEGFA, PPARG, and NOS3. Surprisingly, KEGG pathway enrichment analysis suggested that the herbs may treat hyperlipidemia by influencing the lipid and atherosclerosis pathway and the pathway in cancer. Molecular docking revealed significant affinity between bioactive compounds such as physciondiglucoside and baicalin with proteins involved in cancer pathways. Three active compounds, including 3-beta-hydroxymethyllenetanshiquinone, dan-shexinkum d, and physciondiglucoside have good binding ability with AKT1, PTGS2, and PPARG. The anti-hyperlipidemia activity of herbal medicines may be mediated via regulating proteins with roles in cancer. This study provides further evidence supporting the potential pharmacotherapeutic candidates for the combined treatment of hyperlipidemia and cancer in the future.