The “active metabolite-target-pathway” network revealed that active metabolites such as luteolin from S. miltiorrhiza, Tan IIA from S. miltiorrhiza, puerarin from Pueraria lobata, and β-sitosterol from Pueraria lobata can regulate lipid metabolism and atherosclerosis, the AGE-RAGE pathway in diabetic complications, shear stress and atherosclerosis, and the HIF-1, TNF, and IL-17 pathways to exert anti-MF effects. This evidence concerns the gene HIF1A and atherosclerosis.