A 4-month-old male infant was admitted to our hospital due to recurrent lung infections and fever. He was diagnosed with persistent truncus arteriosus (type AIII) and pulmonary infection based on echocardiography. During the anti-infection treatment, bile-like fluid and feces were drained out from the abdominal cavity, indicating the occurrence of intestinal obstruction and perforation caused by abdominal infection. Emergency exploratory laparotomy was performed under general anesthesia. The risk of heart failure and multiple organ dysfunction is significantly increased during emergency surgery for children with persistent truncus arteriosus. In treating these patients, it is imperative to maintain a balance in systemic pulmonary circulation, ensure adequate fluid resuscitation, and optimally utilize positive inotropic agents to prevent the onset of sepsis-induced shock.