Abstract Resveratrol and quercetin have effects on polycystic ovary syndrome (PCOS). Hence, resveratrol combined with quercetin may have better effects on it. However, because of the limitations in animal and human experiments, the pharmacological and molecular mechanism of quercetin-resveratrol combination (QRC) remains to be clarified. In this research, a systematic pharmacological approach comprising multiple compound target collection, multiple potential target prediction, and network analysis was used for comparing the characteristic of resveratrol, quercetin and QRC, and exploring the mechanism of QRC. After that, four networks were constructed and analyzed: (1) compound-compound target network; (2) compound-potential target network; (3) QRC-PCOS PPI network; (4) QRC-PCOS-other human proteins (protein-protein interaction) PPI network. Through GO and pathway enrichment analysis, it can be found that three compounds focus on different biological processes and pathways; and it seems that QRC combines the characteristics of resveratrol and quercetin. The in-depth study of QRC further showed more PCOS-related biological processes and pathways. Hence, this research not only offers clues to the researcher who is interested in comparing the differences among resveratrol, quercetin and QRC, but also provides hints for the researcher who wants to explore QRC’s various synergies and its pharmacological and molecular mechanism. Subject terms: Reproductive disorders, Medical research Introduction Polycystic ovary syndrome (PCOS) is one of the most common female endocrine diseases characterized by hyperandrogenism, menstrual disorders and infertility. The prevalence of PCOS is estimated at 6–18%^[33]1,[34]2. PCOS is associated with a variety of factors, such as systemic inflammation, endothelial dysfunction, endocrine and metabolic disorders and dyslipidemia^[35]3,[36]4. Currently, lots of evidence has shown that PCOS is usually associated with hyperlipidemia, decreased glucose tolerance, cardiovascular disease, type 2 diabetes, cancer and hypertension^[37]5,[38]6. In clinical, the main pharmacology options of PCOS are anti-androgen, oral contraceptives and so on. However, the treatment of PCOS remains a major challenge in obstetrics and gynecology. For example, metformin, as a first-line treatment for PCOS, can reduce peripheral blood glucose and insulin levels; however, long-term use may result in side effects such as gastrointestinal discomfort. Although the etiology of PCOS is still unclear, plenty of evidence has suggested that hyperandrogenism and inflammation are the key factors^[39]7–[40]10. Evidence also suggests that resveratrol and quercetin, the nature polyphenolic compounds, may be the potential novel drugs for hyperandrogenism. Latest clinical trials have found that resveratrol can significantly reduce ovarian and adrenal androgens, and improve insulin sensitivity^[41]11. Animal experiments also show that in PCOS rat models, resveratrol can improve plasma anti-Mullerian hormone levels, IGF-1 levels and oxidative stress parameters; and it also reduces rat theca-interstitial cell growth in vitro and inhibits insulin-induced rat theca-interstitial cell growth^[42]12,[43]13. Another clinical trial about quercetin shows that quercetin effectively improves adiponectin - mediated insulin resistance^[44]14. And the animal experiments also suggest that in PCOS rat models, quercetin can inhibit Toll-like receptor/NF-κB signaling pathway and improve the ovarian inflammatory microenvironment (Interleukin [IL] 1β, IL-6 and tumor necrosis factor [TNF] -α). Moreover, quercetin can also inhibit phosphoinositide 3-kinase (PI3K) inhibition and decrease CYP17A1 gene expression^[45]15. According to these references, it appears that resveratrol combined