Objective This was a population-based cohort study, to compare the type and structure of intestinal flora in patients with polycystic ovary syndrome (PCOS) with phlegm-dampness syndrome, nonphlegm-dampness syndrome, and normal population. Besides, changes in the intestinal flora and the clinical curative effects of Jiawei Qi Gong Wan on phlegm-dampness syndrome in patients with polycystic ovary syndrome (PCOS) were evaluated. Patients and Methods. A total of 22 patients with PCOS with phlegm-dampness syndrome, 21 PCOS patients with nonphlegm-dampness syndrome, and 20 control volunteers were selected for this study. The general index, sex hormone index, fasting blood glucose (FPG), and serum fasting insulin (FINS) were determined in each of the groups. The intestinal flora of each group was determined by the 16s rDNA high-throughput sequencing technique. Besides, the PCOS with phlegm-dampness syndrome group was treated with Jiawei Qi Gong Wan, and the changes in TCM syndrome, sex hormone index, BMI, WHR, FPG, FINS, HOMA-IR, and intestinal flora were determined before and after treatment. Results PCOS patients with phlegm-dampness syndrome showed characteristics of obesity and insulin resistance. There were several differences in both structure and function of the intestinal flora between PCOS patients with phlegm-dampness syndrome, PCOS patients with nonphlegm-dampness syndrome, and the control group. An imbalance in the intestinal flora may be a key factor in the pathogenesis of PCOS with phlegm-dampness syndrome and also has a specific influence on glucose and lipid metabolism, obesity, and the menstrual cycle in PCOS patients with phlegm-dampness syndrome. Besides, the imbalance is associated with a decrease in the number of butyrate-producing bacteria, an increase in the number of lipopolysaccharide-producing bacteria, and an increase in proinflammatory bacteria. The intestinal flora in PCOS patients with phlegm-dampness syndrome was found to be linked to obesity, impaired glucose tolerance, and hyperandrogenemia. Treatment with Jiawei Qi Gong Wan was found to increase the diversity of intestinal flora, increase the number of intestinal probiotics, and improve the structure and functional genes of intestinal flora which improved the state of insulin resistance, regulated endocrine metabolism, and improved the overall symptoms. Conclusions Intestinal flora imbalance is a key factor in the pathogenesis of PCOS with phlegm-dampness syndrome. Besides, Jiawei Qi Gong Wan improves insulin resistance which is linked to the status of the intestinal flora in PCOS patients with phlegm-dampness syndrome.