BACKGROUND: Bushen Huatan Huoxue Formula (BHHF), a traditional Chinese medicine decoction, demonstrates potential in treating polycystic ovary syndrome (PCOS), a prevalent endocrine disorder in women of reproductive age that is closely associated with obesity and metabolic dysregulation. However, the underlying molecular mechanisms of BHHF's action remain unclear. This study aimed to evaluate the therapeutic efficacy of BHHF in obesity-associated PCOS and investigate its regulatory mechanisms related to metabolic homeostasis. METHODS: In vivo, three-week-old female Sprague Dawley rats were divided into seven groups: control, dehydroepiandrosterone (DHEA), high-fat diet (HFD), model (HFD + DHEA), low-dose BHHF, high-dose BHHF, and metformin. The PCOS model was induced by DHEA injection. BHHF was administered by gastric gavage for four weeks. Body weight, fat volume, glucose tolerance, and insulin sensitivity were measured. Ovarian histology, hormone analysis, RNA extraction, quantitative real-time PCR, protein extraction, western blotting, and proteomics studies were also conducted. In vitro, 3T3-L1 cells were used to assess lipid accumulation, mitochondrial function, and the effects of BHHF-containing serum. RESULTS: BHHF restored reproductive cyclicity and polycystic ovarian morphology, reduced testosterone and anti-Müllerian hormone levels, and increased estradiol levels. It also alleviated weight gain, reduced fat volume, improved glucose tolerance, and enhanced insulin sensitivity. Proteomics analysis revealed that BHHF activated the AMPK signaling pathway and promoted white adipose tissue browning. In vitro, BHHF-containing serum suppressed lipid accumulation and enhanced mitochondrial oxygen consumption. The bioactive components of BHHF-Bushen (BS), Huatan (HT), and Huoxue (HX) -exhibited specific functions. BS improved estrous cyclicity and ovarian morphology; HT regulated glucose and lipid metabolism and promoted adipose browning; and HX modulated mitochondrial bioenergetics and redox homeostasis. CONCLUSION: BHHF exerts multi-targeted therapeutic effects on obesity-associated PCOS by regulating metabolic-reproductive crosstalk. Its components act synergistically, offering a novel therapeutic strategy for PCOS treatment. Future research should focus on identifying core active compounds and optimizing treatment according to individual PCOS phenotypes.