The purpose of the present study was to determine the anti-inflammatory mechanism of moxibustion and acupuncture in the treatment of CD by assessing the effects of moxibustion and acupuncture on the ratio of Th17 and Treg cells and the expression of key related molecules (forkhead box P3 (FOXP3), retinoid-related orphan receptor gamma (RORγt), and interleukin-17 (IL-17)) in the intestinal mucosa of patients with CD. The gene discussed is FOXP3; the disease is Cowden disease.