Objective: To summarize experience in the treatment of complex congenital intestinal atresia in children, so as to investigate the key points and effect of the operation. Methods: Medical notes of 49 children with complex intestinal atresia treated between January 2012 and January 2018 were reviewed. The information of age, sex, age at operation, full-term or premature, birth weight, clinical manifestation, auxiliary examination, preliminary diagnosis, treatment process, discharge diagnosis, pathological results and prognosis of patients were analyzed. Results: All patients underwent surgical treatment, including 42 cases with laparotomy (85.7%) and 7 with laparoscopic surgery (14.3%); 1 case undergoing laparoscopic surgery was converted to laparotomy due to meconium peritonitis. The mean operation time was (147±43) min (70-270 min); the mean fasting time after surgery was (8±3) d (4-16 d); the mean parenteral nutrition time was (12±6) d (3-30 d). Eleven cases were discharged against medical after operation and lost to follow-up. Among rest 38 children, 1 child (2.6%) received intestinal resection and ostomy five days after operation due to gastrointestinal perforation; 1 child (2.6%) received conservative treatment one month later due to adhered intestinal obstruction and left hospital with cure; 1 child (2.6%) received enterodialysis and ileostomy eight days after operation due to anastomotic leak, and received the operation for the closure of fistula after three months; 4 children had complications including fluid and electrolyte disorders, anemia, hypoproteinemia and so on, and recovered after conservative treatments. Postoperative follow-up showed that 1 child with duodenal atresia had lower body weight at 6 month after operation, but the body weight returned to normal when the child was one year old; 1 child with preterm labor of 32 weeks was treated with enteral nutrition, and gradually restored the normal diet after 6 months. Growth retardation was not observed in other children. Conclusion: With active treatment and reservation of normal bowel tube as much as possible during the operation, the prognosis of children with complex intestinal atresia is usually favorable.