INTRODUCTION: Cantrell syndrome is a rare syndrome of congenital defects, which can be complicated by severe pulmonary hypertension and left ventricular diverticulum; it has proved difficult to treat in clinical practice. CASE PRESENTATION: A 6-month-old Han Chinese baby girl weighing 3.5kg was diagnosed, using ultrasonography and radiography, as having Cantrell syndrome complicated by severe pulmonary hypertension. For safety, we divided management into two stages. For the first stage, we dealt with the left ventricular diverticulum and pulmonary hypertension. Three months later, we performed diorthosis for an intracardiac malformation. CONCLUSIONS: Cantrell syndrome with pulmonary hypertension may respond well to this novel two-stage operation, which needs more verification via clinical practice