Objective:To observe the clinical effect and possible mechanism of “Cupai Decoction” in patients of polycystic ovarian syndrome (PCOS) with insulin resistance (IR). MethodsEighty cases of PCOS with IR were randomly divided into the treatment group and control group, 40 cases in each group. The treatment group was orally treated with “Cupai Decoction”,and the control group was orally treated with Diane-35. Both groups were treated for three months and follow-up for three months. The clinical effect was observed and the index changes in endocrine and sex hormone were compared.  Results:①During the trial,two cases among all 80 patients fell off. Finally 78 patients completed the trial,39 cases in each group. ②The total effective rate in the treatment group and control group was 74.36 % and 51.28 %,respectively,the difference was statistically significant and the treatment group was better than the control group(P<0.05). ③Comparison of before and after treatment,the difference on the level of serum homocysteine(Hcy) in the treatment group was statistically significant (P<0.05),but no statistically significant difference in the control group(P>0.05). After treatment,the level of Hcy in the treatment group was obviously decreased compared with the control group,with statistically significant difference (P<0.05). After 3 months follow-up, there was no rebound in the level of Hcy in the treatment group, which was significant decreased compared with treatment before and the control group (P<0.05). ④Comparison of before and after treatment,the differences on the level of LH, LH/FSH in the treatment group and LH,T,LH/FSH in the control group were statistically significant (P<0.05)；After 3 months follow-up, the levels of LH,T,LH/FSH in the control group were rebounded obviously(P<0.05). After 3 months follow-up, the level of LH/FSH in the treatment group was significant lower than that in the control group (P<0.05).  Conclusion:Cupai Decoction shows good effect in the treatment of PCOS with IR. Its mechanism may be achieved by reducing the level of Hcy effectively and continuously and controlling the levels of LH, LH/FSH stably.