Objective: To observe the effects of modified Erchen decoction on reproductive endocrine function and glucose metabolism in patients with phlegm-dampness type of polycystic ovary syndrome (PCOS) complicated with insulin resistance (IR). Methods: A total of 86 patients with PCOS complicated with IR were recruited in this prospective study and divided into two groups according to a random number table with 43 cases in each group. The patients in the control group were treated with a standard western medical recipe, and those in the treatment group were treated with modified Erchen decoction based in addition to the western medicine recipe. All patients received the treatment for 3 menstrual cycles. The observation indictors included traditional Chinese medicine (TCM) syndrome scale scores, serum lipid indicators (total cholesterol (TC), triglyceride (TG), low density lipoprotein cholesterol (LDL-C) and high density lipoprotein cholesterol (HDL-C), insulin resistance indicators (fasting plasma sugar (FPG), fasting insulin (FINS) and homeostasis model assessment of insulin resistance (HOMA-IR)), sex hormone indicators (luteinizing hormone (LH), follicle stimulating hormone (FSH), E-diol (E-2) and testosterone (T)), ovulation and menstrual cycle before and after the treatment. The pregnancy outcomes of two groups were compared. Results: Compared with before treatment, the TCM syndrome scale scores, the levels of TC, TG, LDL-C, LH, FSH, T, FPG, FINS, HOMA-IR and menstrual cycle in both groups were decreased after treatment, and the levels of HDL-C, E-2 and ovulation rate were increased. All the above indicators of the treatment group were recovered to better levels than those of the control group (P<0.05). After 6 months of follow-up, the pregnancy rate in the treatment group was higher than that in the control group (72.09% vs. 51.16%, P<0.05). Conclusion: The combined use of modified Erchen decoction and standard western medicine for patients with phlegm-dampness PCOS and IR can significantly improve their clinical symptoms and insulin resistance, regulate lipid levels and improve the reproductive endocrine function.