Objective To explore the prescription rules of ancient physicians in the treatment of obese polycystic ovary syndrome (PCOS) by data mining, summarize the core prescriptions and drugs and explore the potential material basis and mechanism of core prescriptions using network pharmacology, so as to provide a reference for traditional Chinese medicine (TCM) treatment of obese PCOS. Methods Based on the Chinese Medical Code, a prescription database was established by Excel 2018. The ancient prescriptions of obese PCOS were analyzed by SPSS Modeler 18 and Gephi 0.9.7 software. Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP) was used to obtain the components and targets of the core prescriptions. The Human Gene Database (GeneCard) and Online Mendelian Inheritance in Man Database (OMIM) were used to obtain the disease targets, and then intersection genes of drug targets and disease targets were obtained. Cytoscape 3.7.1 software was used to construct the active components-intersection genes network, and Database for Annovation, Visualization, and Integrated Discovery (DAVID) was used for tissue enrichment analysis. Results A total of 47 prescriptions for obese PCOS were obtained, involving 98 kinds of TCMs. The TCMs with frequency ≥5 were Poria, Rhizoma Pinelliae, Radix Glycyrrhizae, Pericarpium Citri Reticulatae, Radix chuanxiong, Rhizoma Cyperi, Rhizoma Atractylodis macrocephalae, Radix Angelicae sinensis, Rhizoma Atractylodis, Rhizoma Arisaematis, Radix Ginseng, Talcum, Fructus Aurantii, Radix Paeoniae Alba, Rhizoma Coptidis, Radix Rehmanniae, Citri Exocarpium Rubrum, and Fructus Amomi. The core drug pair combination with strong correlation was Rhizoma Pinelliae, Pericarpium Citri Reticulatae, Poria, and Radix Glycyrrhizae (Erchen decoction). A total of 125 components and 218 target genes were obtained from TCMSP database; 2 962 disease target genes were obtained from GeneCard and OMIM, and 149 intersection genes of obese PCOS target genes and core drug target genes were obtained. Network pharmacology showed the active ingredients of the drugs with high degree values included quercetin, kaempferol, and formononetin, and the target genes with high degree values included prostaglandin endoperoxide synthase 2, estrogen receptor 1, and androgen receptor. The tissue enrichment analysis showed that the intersection target genes were mainly enriched in the placenta, liver, lung, and epithelium. Conclusion The data mining results suggest that the main principle of treating obese PCOS is to dry dampness, remove phlegm, benefit Qi, and strengthen spleen, while supplemented with drugs that nourish blood and regulate menstruation. The network pharmacology results have verified the results of ancient literature analysis, suggesting that flavonoids may improve obese PCOS by modulating hormone receptors.