Background <p>Polycystic ovary syndrome (PCOS) is a common endocrine and metabolic disorder that severely impairs female fertility. Zuogui pill (ZGP) is clinically used for the treatment of reproductive disorders such as menopause syndrome and premature ovarian failure, improving female reproductive health. However, the mechanism of its action in treating PCOS remains unclear. This study aimed to investigate the mechanism of ZGP in treating PCOS based on liquid chromatography-mass spectrometry (LC-MS) and proteomics.</p> Methods <p>LC-MS was utilized to analyze and identify the active components of ZGP. A PCOS rat model was established using a high-fat diet combined with letrozole to assess the efficacy of ZGP. Serum hormone levels in rats were detected using ELISA, and ovarian morphology was examined via hematoxylin and eosin staining. 4D-DIA-based proteomics was performed on ovarian samples from rats, and a combined analysis with network pharmacology was conducted to identify key pathways and their targets. Finally, Western blot analysis was used to validate the analytical results.</p> Results <p>A total of 31 components of ZGP were identified through LC-MS analysis combined with the TCMSP database. In the PCOS rat model, ZGP significantly improved obesity and ovarian tissue damage, regulated serum sex hormone secretion levels. Through a combined analysis of network pharmacology and 4D-DIA-based proteomics, the potential mechanism of ZGP in improving PCOS was determined to be the mitogen-activated protein kinase (MAPK) signaling pathway. WB analysis revealed that ZGP reversed the expression levels of p-ERK1/2 and p-JNK.</p> Conclusion <p>This study demonstrates that ZGP may exert a therapeutic effect on PCOS through the MAPK signaling pathway.</p>