Objective To evaluate the safety and effect of seromuscular layer anastomosis in small intestinal suture. Methods Forty patients with hepatobiliary and pancreatic diseases undergoing biliojejunostomy or cystojejunostomy were randomly divided into seromuscular layer anastomosis group (n=20) and two-layer anastomosis group (n=20) before operation， which received Roux-en-Y end-to-side jejunal seromuscular layer anastomosis and two-layer anastomosis, respectively. Intestinal anastomotic complications and other indexes such as anus venting time were recorded in each group. Results Neither group had intestinal anastomotic complications such as leakage, stricture, obstruction and hemorrhage. Time of venting to normal were (3.6±0.9) d and (3.6±0.8) d in seromuscular layer and two-layer anastomosis group respectively, there was no significant difference between them (Pgt;0.05). Conclusion Seromuscular layer anastomosis is a safe and effective method of small intestinal anastomsis.