Introduction: Polycystic ovary syndrome (PCOS) is a complex endocrine disorder of women. Most of PCOS women have great pressure because of infertility. Aim of our study is to observe the clinical efficacy of acupuncture therapy on the treatment of anxiety disorder in patients with PCOS and compare the therapeutic effect differences between acupuncture therapy and Clomiphene Citric (CC) therapy. Materials and methods: 90 PCOS patients were allocated into acupuncture combined with CC group (group A), acupuncture group (group B) and CC group (group C) randomly, 30 cases in each group. The acupoints were Ganshu (BL18), Shenshu (BL23), Zhongwan (CV12), Shuifen (CV9), Guanyuan (CV4), Zhongji (CV3). Back-shu points were used alternatively. Fast rotating needling insertion method and mild reinforcing-reducing manipulation were operated. The needle retaining time was 30 minutes. The patients in group A and group B received acupuncture therapy 3 times per week. The CC was taken on the 5th-9th day of menstrual cycle. All the patients were treated for 3 months and followed-up for 1 month. The self-rating anxiety scale (SAS) and ovulation rate of the 3 groups were counted. Results: 3 cases dropped out in the trail. The SAS scores declined both of group A and B after treatment. The ovulation rates of group A, B and C were as follows: 86.21%, 66.67% and 69.64%. The clinical efficacy of group A was higher than the other groups (P<0.05). Discussion: Acupuncture therapy can enhance ovulation rate of PCOS patients effectively as well as CC therapy. But it is a better method to improve the anxiety disorder than CC therapy. The combined application of acupuncture therapy and CC therapy has better curative effect, which should be widely spread in clinics.