<p>Functional constipation (FCon) is characterized by disrupted brain-gut communication, representing a core pathophysiological mechanism. Physical exercise, a safe and cost-effective intervention, has been proven efficacy in ameliorating constipation symptoms and is a vital self-management strategy. Tai Chi, a traditional Chinese exercise, has been demonstrated to benefit both the gastrointestinal tract and the brain. However, the potential mechanism underlying Tai Chi’s gastrointestinal regulatory effects through enhancement of brain-gut communication remains to be elucidated. This randomized controlled trial enrolled 80 FCon patients and 32 healthy subjects. Patients were randomized to either Tai Chi or aerobic exercise group. Both groups participated in four 60-min sessions per week for 8 weeks. Outcome measures included symptom severity, quality of life, autonomic neural function (assessed via heart rate variability), and brain activity. Both groups exhibited significant improvements in clinical symptoms, mood states, and heart rate variability post intervention. Tai Chi showed a marginal superiority over aerobic exercise in alleviating clinical symptoms. Notably, the neuroimaging findings suggested that Tai Chi effectively modulated the abnormal functional connectivity of the anterior insula within the central autonomic network in FCon patients, which was not observed in the aerobic exercise group. These modulations correlated with clinical symptoms and heart rate variability indices. Our study suggests that Tai Chi may facilitate the coordination between central and autonomic nervous functions by modulating functional connectivity of the anterior insula within the central autonomic network, and promoting sympathetic/parasympathetic balance, thereby enhancing the brain-gut communication. This may represent the underlying mechanism by which Tai Chi exerts gastrointestinal modulation to improve FCon symptoms.</p><p>Trial registration: ChiCTR1800019781.</p>