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Background Polycystic ovary syndrome with insulin resistance (PCOS-IR) is recognized as one of the most challenging subtypes of PCOS to treat due to its intricate pathogenesis and significant individual variability. Although Metformin, as a first-line medication, can ameliorate blood glucose levels and enhance insulin sensitivity, its efficacy in regulating hormonal imbalances and improving ovarian function is limited. Additionally, its gastrointestinal side effects often hinder patient adherence. Objective To evaluate the efficacy and safety of Yishen Quzhuo Formula compared to metformin in the treatment of PCOS-IR. Methods A prospective study enrolled 102 PCOS-IR patients from June 2022 to October 2023 at the Department of Gynecology, Beijing Hospital of Traditional Chinese Medicine, Capital Medical University. Patients were randomly assigned in a 2∶1 ratio to the experimental group (n=68) treated with Yishen Quzhuo Formula or the control group (n=34) treated with metformin. The comparison was made between the two groups in terms of ovulation rate, pregnancy rate, sex hormones [follicle-stimulating hormone (FSH), luteinizing hormone (LH), LH/FSH ratio, testosterone (T), anti-Müllerian hormone (AMH) ], glucose and lipid metabolism indicators, BMI, waist-hip ratio (WHR), and incidence of adverse reactions. Results After treatment, the basal body temperature (BBT) ovulation rate in the experimental group increased compared to before treatment (P0.05). After treatment, both groups showed a decrease in LH/FSH compared to before treatment (P0.05). After treatment, the waist circumference of the control group was lower than that of the experimental group (P0.05). During treatment, adverse reactions such as hypoglycemia, fatigue, epigastric discomfort, and diarrhea occurred in patients, with a lower incidence of adverse reactions in the experimental group (5/68, 7.35%) than in the control group (15/31, 48.39%) (χ2=20.404, P