Polycystic ovary syndrome (PCOS) is a common endocrine disease in women, potentially causing ovarian infertility for women at gestational age. Huatan Tongjing Decoction is commonly used to treat PCOS; however, the involved molecular mechanism has not been fully understood. In this study, the active components of Huatan Tongjing Decoction and potentially targeted proteins were downloaded from the Traditional Chinese Medicine Systems Pharmacology (TCMSP) database. PCOS-related genes were accessed from Malacards database. STRING database was utilized to construct a protein-protein interaction (PPI) network based on the PCOS-related genes and the predicted targets. Subsequently, the PPI network was subjected to Random walk with restart (RWR). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed on top 50 genes with the high affinity scores to the drug targets. Subsequently, based on the predicted drug components and targets, a component-gene interaction network was constructed. Finally, the most central drug targets were selected, and the corresponding compounds were subjected to molecular docking and dynamic simulations to examine their bindings. The 122 main active components and 246 potential targets of Huatan Tongjing Decoction were obtained from TCMSP, and a total of 259 nodes and 1919 interactions were acquired from the PPI network. The top 50 genes were mainly enriched in response to peptide hormone function and PI3K-Akt signaling pathway. Molecular docking and dynamic simulations predicted that MMP-quercetin interaction played an important role in the treatment of PCOS using Huatan Tongjing Decoction. Luteolin and quercetin in Huatan Tongjing Decoction potentially bound MMP9 and served as active components. This study preliminarily suggested the efficacy of Huatan Tongjing Decoction against PCOS in molecular degree.© 2022 John Wiley & Sons Ltd.