Background: Benign prostatic hyperplasia (BPH) is one of the most common urological disease and often associated with lower urinary tract symptoms (LUTS) in elderly men. Chinese acupuncturists found that deep acupuncture at Qugu point (CV2) can effectively relieve urination difficulties and improve quality of life of patients with troublesome BPH/LUTS. However, there are currently insufficient scientific evidence and well-designed trials to support its effect as well as safety in the treatment of BPH/LUTS. Therefore, this study protocol is designed to evaluate the effectiveness and safety of deep acupuncture at CV2 for men with BPH/LUTS.Methods: A single-center, randomized, subject-and assessor-blinded, placebo-controlled trial will be conducted in an outpatient acupuncture department in Beijing, China. A total of 120 subjects (50-80 yr) will be randomized to one of three balanced groups: deep acupuncture group 1 (deep acupuncture at CV2 with needle tip reaching the prostate capsule), deep acupuncture group 2 (deep acupuncture at CV2 with needle tip 10mm away from the prostate capsule), and sham acupuncture group (sham acupuncture with non-penetrating needle) in a ratio of 1:1:1. The study period for each subject will be 4 months, including 4 weeks baseline observation period, 4 weeks intervention period, and 8 weeks follow-up period. All subjects will receive 10 treatments during the intervention period. Subjects in deep acupuncture groups will be measured the needle depth and angle by computerized tomography (CT) in their first treatment. The primary outcome is the change in International Prostate Symptom Score. Secondary outcomes include quality of life, maximum urinary flow rate, and post-void residual.Discussion: The objectives of this study include: 1) to assess the efficacy of deep acupuncture at CV2 in the treatment of BPH; 2) to evaluate the safety of acupuncture at CV2 by measure the needle depth and angle under CT. This study will provide an evidence-based recommendation for acupuncture at CV2 in the treatment of BPH.Trial registration: Registered on 18 January 2020. Chinese Clinical Trials Register, ChiCTR2000029203.