To evaluate the effect of electro-acupuncture on Zusanli (ST 36), Guanyuan (RN 4) in patients with sepsis, and explore its mechanism in term of immune regulation. In this prospective randomized controlled trial, 60 patients with sepsis were randomly assigned to the control group and the intervention group equally by block randomization. Patients in the control group received routine treatment and those in the intervention group received electro-acupuncture at bilateral Zusanli and Guanyuan in addition to routine treatment, respectively. The mortality at 28 days, Acute Physiology and Chronic Health Evaluation (APACHE)-II score were compared to evaluate the effect, and the levels of T cell subsets (CD3+, CD4+, CD8+, CD4+/CD8+) and monocytes of human leukocyte antigen (HLA)-DR using flow cytometry were compared to explore the mechanism of this combined treatment. Fifty-eight patients completed the trial with 29 in each group. There was no significant difference of mortality in the 28th day between the two groups, with 5 death of 29 patients in the intervention group (17.2%) and 9 of 29 in the control group (31.0%). After treatment, APACHE-II score of both groups was significantly decreased, however, score of the intervention group was lower than the control group (13.28 +/- 7.07 vs. 17.10 +/- 5.83; P < 0.01). The levels of CD3+, CD4+, CD8+ and CD4+/CD8+ ratio of the intervention group improved after treatment and were higher than the control group (59.71%+/- 11.94% vs. 52.54%+/- 11.86%; 36.46%+/- 7.60% vs. 31.58%+/- 10.23%; 18.40%+/- 8.82% vs. 23.07%+/- 7.30%; 2.38 +/- 1.14 vs. 1.54 +/- 0.80, respectively; all P < 0.05). The expression of HLA-DR significantly increased after treatment in the intervention group than that in the control group (7.28%+/- 9.26% vs. 1.27%+/- 7.00%; P < 0.01). Electro-acupuncture at Zusanli and Guanyuan could improve clinical curative effect in patients with sepsis, which might be achieved by regulation of the immune system.