Objective: To evaluate the efficacy of Cangfu Daotan Decoction and Zhibai Dihuang Decoction in the differential treatment of polycystic ovary syndrome (PCOS), based on the core indicator target evaluation. Methods: Using a random number table method, 6 rats were randomly selected from 54 female SD rats as the blank group (no modeling). The remaining rats were randomly divided into groups for the construction of obese PCOS and non-obese PCOS models, with 24 rats in each category. Each model category was further divided into the control group (obese control group/non-obese control group), the Diane-35 group, the Cangfu Daotan Decoction group and the Zhibai Dihuang Decoction group, with 6 rats in each group. The rat morphology, body mass, estrous cycle, ovarian morphology, serum sex hormones, and glucose and lipid metabolism levels were compared. Results: After modeling, except for the blank group, the rats in both the obese and non-obese control groups lacked a regular estrous cycle. The obese PCOS rats exhibited characteristics of spleen deficiency and phlegm-dampness syndrome, while the non-obese PCOS rats showed characteristics of kidney yin deficiency syndrome. After modeling, serum testosterone (T), luteinizing hormone (LH), fasting blood glucose (FBG), fasting insulin (FINS), total cholesterol (TC), triglyceride (TG), and low-density lipoprotein cholesterol (LDL-C) in the obese and non-obese control groups were significantly higher than those in the blank group. LH in the non-obese control group was significantly higher than in the obese control group, while TC, TG, and LDL-C in the obese control group were significantly higher than in the non-obese control group (all P<0.05). After administration, serum T and LH in the Diane-35 group and Cangfu Daotan Decoction group were significantly lower than in the obese control group, and FINS, TC, TG, LDL-C, ovarian volume, and mass in the Cangfu Daotan Decoction group were lower than in the obese control group (all P<0.05). In non-obese PCOS rats, after administration, serum T and LH in the Diane-35 group and Zhibai Dihuang Decoction group were significantly lower than those in the non-obese control group, and FINS, TG, LDL-C, ovarian volume, and mass in the Zhibai Dihuang Decoction group were lower than those in the non-obese control group (all P<0.05). Conclusions: This study experimentally confirms that obesity can serve as a typical characteristic for the differential diagnosis of PCOS. The treatment of obese PCOS with Cangfu Daotan Decoction and non-obese PCOS with Zhibai Dihuang Decoction yields significant effects. This highlights the wisdom of the traditional Chinese medicine principle of "treating the same disease with different methods" and provides animal experimental data supporting the syndrome differentiation and classification treatment of PCOS in traditional Chinese medicine.