Abstract: Objective To explore the clinical effect of bacillus subtilis for assisted treatment of severe acute pancreatitis (SAP). Methods One hundred and thirty-eight patients with SAP from January 2008 to October 2013 in Navy General Hospital were randomly divided into two groups: study group (common therapy and bacillus subtilis) and control group (common therapy). Symptoms, trypsin, hospital time and complications of patients with SAP were observed. Acute physiology and chronic health evaluation (APACHEⅡ) score, CT severity index (CTSI) score, gastrointestinal function score of patients on the first day and 2 weeks after admission and treatment efficiency were analyzed. Results The time of amylase resume, abdominal pain and distention release and hospitalization of patients in study group were 6.2±3.8 d, 6.8±4.9 d, 20.8±6.8 d, 26.7±12.8 d, and 29.7±15.4 d, respectively, which were significantly shorter than control group (P< 0.05). The gastrointestinal function score and APACHEⅡscore of patients in study group were 0.6±0.3 and 4.2±1.9, respectively, which were significantly lower than control group (0.8±0.5 and 5.4±3.4) on the two-week of admission (P< 0.05), while the CTSI score in two groups had no significant difference (P> 0.05). The treatment efficiency of study group was higher than control group (79.2% vs 63.6%, P< 0.05). Incidence of complications of study group was lower than control group (66.7% vs 84.8%, P< 0.05). Conclusion During the treatment of SAP, bacillus subtilis assistant treatment can shorten hospitalization time, improve the recovery of gastrointestinal function and raise the treatment effect, which plays an important role in reducing complications and improving prognosis.