Background: Previous studies suggested that acupuncture was a promising adjunctive treatment for asthma. However, the underlying mechanism of acupuncture for asthma remains unclear. The aim of the present trial is to explore whether and how specific meridian acupuncture works in quality of life and symptomatic improvement by modulating brain function in patients with asthma. Methods/design: This is a randomized controlled functional brain imaging trial currently being conducted in Sichuan, China. In total, 48 patients with mild to moderate persistent asthma will be recruited randomly and allocated to either of two acupuncture groups: acupuncture at the lung meridian or acupuncture at the heart meridian. The treatment period will last 4 weeks. The Asthma Quality of Life Questionnaire is the primary outcome. The Asthma Control Test, peak expiratory flow rate, forced expiratory volume in 1 s, Montreal Cognitive Assessment, Zung Self-rating Anxiety Scale, and Zung Self-rating Depression Scale will also be used to assess the clinical efficacy of different interventions. Functional magnetic resonance imaging (fMRI) will be performed to detect cerebral activity changes in each group. The clinical data and fMRI data will be analyzed between groups, then, the Pearson correlation analysis will be used to assess the association between the changes of cerebral activity features and the improvement of clinical outcomes in each group. Discussion: The present study has been established on the basis of the "meridian-viscera relationship" theory of traditional Chinese medicine and the modern central mechanism of acupuncture. The results of this trial would be useful to identify the efficiency of the specific meridian acupuncture for asthma. The investigation of its central mechanism would further expand knowledge of acupuncture for asthma.