The patient was a 7-day-old male neonate. He was diagnosed with pulmonary atresia (PA), ventricular septal defect (VSD), and patent ductus arteriosus (PDA) by echocardiography due to severe cyanosis after birth. The patient was admitted to our hospital after an emergency tracheal intubation, and an emergency PA correction surgery was subsequently carried out. During the operation, it was found that the patient had a small right ventricle, connections between the right ventricular myocardial sinusoids and intramural coronary artery branches, a lack of effective aorta-coronary communication, and an underdeveloped central confluence of the left and right pulmonary arteries. As a result, a modified systemic to pulmonary artery shunt surgery was performed, and the PDA was ligated. Delayed sternal closure was performed due to significant myocardial edema after the operation. He was then transferred to the cardiac intensive care unit (CICU) with mechanical ventilation and treatment of cardiovascular medications, creatine phosphate for myocardium nourishment, low-molecular-weight heparin calcium for anticoagulation, and antibiotics for infection prevention. The sternum and incision were closed 3 days later. Although the preoperative diagnosis was made by echocardiography in this case, intraoperative exploration showed abnormal coronary perfusion and significant myocardial edema, which led to palliative surgery. The medical team must focus on the cardiac anatomy and coronary development of children with PA.