OBJECTIVE: This study aimed to investigate the clinical effects and underlying mechanisms of Hu’s AnGeng Decoction combined with Femostom in treating menopausal syndrome (MD) associated with Kidney Yin deficiency and disharmony between the heart and kidney, to provide a safe and effective therapeutic option. METHODS: A total of 324 menopausal participants were randomly allocated into three groups: An experimental group receiving Hu’s AnGeng Decoction combined with Femostom (1/10mg) (n=108), control group 1 receiving only Hu’s AnGeng Decoction (n=108), and control group 2 receiving Femostom (1/10mg) only (n=103). Using the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP), TCM-ID, and GeneCards, we retrieved the active ingredients and target proteins of Hu’s AnGeng Decoction along with MD-related targets. A protein–protein interaction (PPI) network was constructed, followed by gene ontology (GO) function enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. RESULTS: The experimental group exhibited significantly better scores in the Modified Kupperman Index (mKI), Follicle-Stimulating Hormone (FSH), and estrogen (E2) levels compared to both control group 1 and control group 2. A total of 119 targets related to Hu’s AnGeng Decoction were identified, along with 17 genes associated with MD, and three common targets were determined through Venny 2.1 analysis. The PPI network highlighted three key targets through topological analysis. GO and KEGG enrichment analyses indicated multiple disease-relevant pathways. Conclusion: Hu’s AnGeng Decoction significantly alleviates MD, likely through active components such as quercetin, beta-sitosterol, naringenin, and beta-carotene, which may exert therapeutic effects by modulating key targets such as estrogen receptor 2 (ESR2), CYP1B1, and AR. This study identified 119 drug target genes and 17 target genes related to menopausal symptoms, illustrating the integrative therapeutic potential of Hu’s AnGeng Decoction.