Objective:To observe the clinical efficacy and possible mechanism of therapy of tonifying kidney and resolving phlegm and clearing heat(Cupai Decoction)in the treatment of polycystic ovarian syndrome(PCOS)with insulin resistance(IR).Methods100 patients were randomly divided into the treatment group and control group,50 cases in each group.The treatment group was treated with the therapy of tonifying kidney and resolving phlegm and clearing heat(Cupai Decoction),and the control group was treated with metformin,folic acid and Vit B,12,. The treatment course in both groups was 5 months with five-month follow-up. The clinical efficacy was observed,and the changes on the oxidative stress related indexes,sex hormone related indexes and index of homeostasis model assessment for insulin resistance(HOMA-IR)were compared.  Results:①Finally 97 patients completed the trial,among 49 cases in the treatment group and 48 cases in the control group ②The clinical total effective rates were 89.8% in the treatment group and 25.0% in the control group. There was statistically significant difference on the clinical efficacy between the two groups,and the clinical efficacy of the treatment group was significantly better than that of the control group(P,<,0.05). ③After treatment,there were no statistically significant differences on the levels of superoxide dismutase (SOD) and malondialdehyde (MDA) between the two groups(P＞0.05)；but there was statistically significant difference on the glutathione peroxidase (GSH-Px) level between the two groups,and the GSH-Px level of the treatment group was obviously higher than that of the control group(P,<,0.05). After five-month follow-up,the levels of SOD and GSH-Px in the treatment group were significantly increased compared with treatment before,and the MDA level in the treatment group was significantly decreased compared with treatment before(P,<,0.05). After five-month follow-up,the MDA level of the treatment group was obviously lower than that of the control group(P,<,0.05). ④Compared with treatment before,the levels of testosterone (T),luteinizing hormone (LH) / follicle stimulating hormone (FSH) and HOMA-IR index were obviously decreased in the treatment group(P,<,0.05),and the HOMA-IR index was obviously decreased in the control group(P,<,0.05). After treatment,the T level of the treatment group was obviously lower than that of the control group(P,<,0.05). After five-month follow-up,the levels of T and LH/FSH in the treatment group were obviously decreased compared with treatment before(P,<,0.05). After five-month follow-up,the levels of T and LH/FSH in the treatment group were obviously lower than those in the control group(P,<,0.05),but there was no statistically significant difference on the HOMA-IR index between the two groups(P＞0.05). ⑤There was statistically significant difference on the incidence rate of adverse reaction between the treatment group and control group,and the incidence rate of treatment group(0/49)was obviously lower than that of the control group(8/48)(P,<,0.05).  Conclusion:The therapy of tonifying kidney and resolving phlegm and clearing heat(Cupai Decoction)shows good efficacy in the treatment of polycystic ovarian syndrome with insulin resistance. Its mechanism may be associated with the sustained and effective reduction on the level of oxidative stress in patients.