Objective Objective To evaluate the efficacy of Heqi San combined with metformin in the treatment of obese polycystic ovary syndrome (PCOS). Methods A total of 60 patients with obese polycystic ovary syndrome who met the inclusion criteria were randomly divided into 2 groups, 30 patients in each group. The control group was treated with metformin, and the treatment group was treated with Heqi San on the basis of the control group. Both groups were treated for 3 months. The FPG was determined by glucose oxidase method, and fasting insulin (FINS), TC, TG, LDL-C, HDL-C level were measured by radio immunoassay, and the insulin resistance index (IR) was measured by the method of HOMA-IR. The luteotropic hormone (LH), pro follicle stimulating hormone (FSH) and testosterone (T) were detected by the automatic electrochemical light detector, and the ratio of LH/FSH was calculated. The ovarian volume and body mass index changes and clinical effect were evaluated. Results After treatment, the BMI (20.09 ± 3.12 kg/cm2 vs. 23.39 ± 1.43 kg/cm2, t=6.889), FPG (4.44 ± 0.17 mmol/L vs. 4.74 ± 0.16 mmol/L, t=6.945), FINS (10.69 ± 2.41 IU/L vs. 16.29 ± 5.95 IU/L, t=4.778), TC (3.91 ± 0.50 mmol/L vs. 4.20 ± 0.39 mmol/L, t=2.505), LDL-C (2.64 ± 0.63 mmol/L vs. 3.18 ± 0.62 mmol/L, t=3.346), LH (8.70 ± 2.44 U/L vs. 10.27 ± 2.69 U/L, t=2.934), the ratio of LH/FSH (1.33 ± 0.58 vs. 2.18 ± 0.56, t=5.775), T (1.73 ± 0.74 nmol/L vs. 2.95 ± 1.10 nmol/L, t=5.040) and ovarian volume (12.61 ± 2.29 mm3 vs. 14.26 ± 2.52 mm3, t=6.982) in the treatment group were significantly lower than those in the control group (P<0.01 or P<0.05). The FSH (7.33 ± 2.28 U/L vs. 5.95 ± 1.20 U/L, t=2.934) in the treatment group were significantly higher than those in the control group (P<0.05). The total effective rate in the treatment group was 83.3% (25/30) and 63.3% (19/30) in the control group. The difference between the 2 groups was statistically significant (χ2=3.068, P=0.050). Conclusions The Heqi San combined with metformin can effectively improve the body mass index, glucose metabolism, lipid metabolism index and sex hormone level, and reduce the volume of ovary in patients with PCOS, and the curative effect is better than that of oral metformin alone.