Hypertrophic cardiomyopathy (HCM) and hypertension often coexist, sharing common etiological factors and pathological mechanisms. Both traditional and modern medicine have explored food and medicine products for their treatment This study examines the therapeutic potential and mechanisms of Achyranthis bidentatae radix and Saururus chinensis, two natural products used in food and medicine homology, in addressing HCM and hypertension. Bioinformatics and computer-aided drug design (CADD) approaches were utilized to identify active ingredients and mechanisms. In vivo and ex vivo experiments were performed to validate the pharmacological effects under conditions mimicking HCM and hypertension. Disease-related genes were identified using GeneCards and DisGeNET, while key components were identified via Traditional Chinese Medicine Systems Pharmacology Database (TCMSP). A total of 62 disease-related genes were identified, with 20 significant components for A. bidentatae radix and 5 for S. chinensis Intersection analysis highlighted 18 common target genes involved insulin-like growth factor 1 receptor (IGF1R), insulin receptor (INSR), insulin (INS), Matrix Metallopeptidase 9 (MMP9), signal transducer and activator of transcription 3 (STAT), were confirmed through real-time PCR in vivo. Molecular docking studies demonstrated direct interactions between quercetin and IGF1R, INSR, MMP9, and between inophyllum E and INS. Molecular dynamics simulations showed favorable binding of quercetin with INSR. Quercetin exhibited promising drug-likeness and therapeutic potential in angiotensin II-treated cardiomyocytes. In conclusion, quercetin, identified as active component in A. bidentatae radix and S. chinensis, shows promising therapeutic effects against HCM and hypertension. These findings highlight the potential of these natural products in cardiovascular disease management through targeted molecular interactions. Future research should explore the nature products with long-term effects in comprehensive cardiovascular disease treatment.