The purpose of this study was to investigate the effect of electroacupuncture (EA) and moxibustion on promoting neutrophil apoptosis. A rat model of ulcerative colitis was established by immunological methods using human colonic mucosa as antigen. All rats were randomly assigned to the model control (MC) group, EA group, or herbs-partition moxibustion (HPM) group. Normal rats were used as the normal control (NC) group. Peripheral blood mononuclear cells (PBMCs) from all rats and circular neutrophils from NC rats were isolated and cultured. Circular neutrophils were incubated with cultured supernatants of PBMCs from the MC, NC, EA, and HPM groups, respectively. Neutrophil apoptosis and concentration of IL-1beta, IL-6, and TNF-alpha from induced cultured supernatants were detected by cell cytometry and ELISA, respectively. Compared with MC, HPM, and EA rats, mucosal inflammatory lesions abated remarkably. No hyperemia or edema was seen in the lamina propria, inflammatory cell infiltration decreased, neutrophil infiltration disappeared, and epithelial and crypt cells proliferated and repaired the ulceration of the mucosa. Neutrophil apoptosis was promoted. Concentrations of IL-1beta, IL-6, and TNF-alpha were decreased, respectively. We conclude that EA and HPM therapy can improve ulcerative colitis rats histologically, which may be due to promoting neutrophil apoptosis and down-regulating monocyte cytokines. EA and moxibustion are effective for treating ulcerative colitis.