Background: Functional constipation (FC) is highly prevalent in the general population of the world and has a substantial negative impact on the health-related quality of life of individuals. Many clinical trials have indicated that acupuncture is effective in the treatment of FC. However, the sample sizes of these previous studies were too small. Furthermore, there are no reports investigating the relationship between the stimulation parameter and the therapeutic effect. We therefore designed a multicenter randomized controlled trial to address these problems and hopefully provide a more conclusive answer to these questions. Methods: Participants will be included if they meet all of the following conditions: (1) diagnosed with functional constipation according to the Roman III standard; (2) aged between 18 and 65 years; (3) not taking any drugs that promote gastrointestinal movements at least during the 1 week prior to randomization; (3) willing to sign an informed consent form; (4) willing to return to the study site for their study visits. The participants will be randomly assigned to three groups in a 1: 1: 1 ratio: high current intensity group, low current intensity group, and mosapride citrate control group. The total study period is 9 weeks for each patient, 1 week for baseline, 4 weeks for treatment, and 4 weeks for follow-up. The primary outcome in this trial is the number of defecating events per week. The secondary outcomes will include the shape and properties of the stool, intensity of defecating difficulty, Patient Assessment of Constipation Quality of Life (PAC-QOL), MOS item Short Form health survey (SF-36), Self-Rating Anxiety Scale (SAS), and Self-Rating Depression Scale (SDS). Discussion: This study will provide significant evidence for the application of acupuncture in FC and will identify a suitable stimulation parameter for treatment.