Objective. To compare the impacts of electroacupuncture (EA) and mild moxibustion (Mox) on patients with irritable bowel syndrome (IBS). Method. Eighty-two IBS patients were randomly allocated into EA group (n = 41) and Mox group (n = 41) and received corresponding interventions for four weeks. Before and after the treatment, the Visual Analogue Scale for Irritable Bowel Syndrome (VAS-IBS) was used to evaluate the gastrointestinal symptoms and mental well-being; and the expression of serotonin (5-hydroxytryptamine, 5-HT), 5-HT3 receptor (5-HT3R), and 5-HT4 receptor (5-HT4R) in sigmoid mucosal tissue were detected. Results. Both EA and Mox can radically improve the total VAS-IBS score (P < 0.05), and EA was found to be more effective in ameliorating the symptom of constipation, while Mox was found to be more effective in ameliorating the symptom of diarrhoea. The abnormal expressions of 5-HT, 5-HT3R, and 5-HT4R in both groups were significantly improved after the treatments (all P < 0.05), and EA was superior to Mox in regulating the abnormally decreased 5-HT4R expression in IBS patients with constipation (P < 0.05). Conclusion. Electroacupuncture and mild moxibustion were both effective in improving IBS symptoms and modulate abnormal expressions of 5-HT, 5-HT3R, and 5-HT4R in the colonic tissue.