Abstract Background Polycystic ovary syndrome (PCOS) is one of the most common endocrine diseases for women. Acupuncture is widely used for the infertile female because of it is non-invasive and has fewer side effects, but the powerful evidence for the clinic is still insufficient. Our study intends to explore the effect of manual acupuncture (MA) in the infertile female with PCOS. Methods This study is a randomized, sham-controlled, patient-and assessor-blinded trial and aims to evaluate the effect of MA in women with PCOS and infertility. We will recruit 86 women aged 20–40 years with a diagnosis of infertility with PCOS. Participants will be randomly allocated in a 1:1 ratio to the MA group and the sham acupuncture (SA) group. Both groups will receive real herbal medicine treatment as a basic treatment twice a day for three menstrual cycles, the MA group receive real acupuncture treatment and the SA group received placebo acupuncture treatment (non-penetrating). All patients will receive acupuncture treatment twice per week for three menstrual cycles. The primary outcome is pregnancy rate and secondary outcomes include ovulation rate, sex hormones, insulin resistance index (IRI), PCOS symptoms, and Traditional Chinese Medicine (TCM) syndrome scores. Outcome measures will be collected at baseline, each menstrual cycle, the end of treatments, and six months after the last acupuncture treatment. The present protocol followed the SPIRIT guidelines and fulfilled the SPIRIT checklist. Discussion This study will be conducted to compare the efficacy of MA versus SA. This trial will help to evaluate whether MA is effective in increasing pregnancy and ovulation rates of the infertile female with polycystic ovary syndrome. Trial registration Chinese Clinical Trial Registry, ChiCTR1800014997 . Registered on 27 February 2018.