We reported a case of a six-year-old boy diagnosed of single ventricle, pulmonary atresia and interrupted inferior vena cava. After modified Blalock-Taussig shunt and bidirectional Glenn procedure, he received the Fontan procedure. The Fontan procedure was done through a unilateral thoracotomy, using an autologous pericardial conduit to connect hepatic vein and azygos vein. The result of short-term follow-up was satisfactory.