The integration of metabolomics and network pharmacology revealed that R. Scrophulariae might mainly regulate the IL6-APOA1-cholesterol pathway, AKT1-THEM4-palmitic acid pathway, AKT1-THEM4-hexadecanoate (n-C16:0) pathway, NOS3-LYPLA1-palmitic acid pathway and NOS3-LYPLA1-hexadecanoate (n-C16:0) pathway to play a role in the treatment of hyperthyroidism. Here, NOS3 is linked to hyperthyroidism.