Objective To review and summarize the experience in the treatment of pediatric critical complex precordial disease by lateral access and external conduit Fontan procedure. Methods A total of 128 children with complex intracardiac malformations were admitted for modified Fontan operation from January 2000 to December 2006. There were 76 male cases and 52 female cases. The ages ranged from 1.9 to 16.5 years (mean 6.2±3.8), and the weights ranged from 8 to 62 Kg (mean 19±5.5 Kg). The main types of disease were single ventricle (SV) 59 cases; double outlet right ventricle (DORV) 25 cases, etc. First-stage Fontan surgery was performed in 87 cases; second-stage Fontan surgery was performed in 41 cases, and the time interval between the second surgery was 0.8-7.3 years (3.9±2.8 ), and the first surgery was unilateral Glenn (12 cases), bilateral bidirectional Glenn (8 cases), etc. The Fontan group (LT group) with endocardial access (LT) was performed in 89 cases, and the Fontan group (ECC group) with external conduit (ECC) was performed in 39 cases. Preoperative 2D Doppler ultrasound was performed in all cases, 11 cases had additional MRI, and 30 cases had cardiac catheterization and cardiovascular angiography. The age of patients in the LT group was significantly lower than that in the ECC group. 32 patients developed low cardiac output syndrome, and 11 of them underwent peritoneal dialysis due to impaired renal function (urine output was restored after 2-5 days of dialysis). the incidence of postoperative cardiac rhythm disturbances was significantly higher in the LT group than in the ECC group. No serious complications and no death occurred during the outpatient follow-up of 3 months to 2 years. Conclusion The incidence of postoperative cardiac rhythm disturbances was significantly higher in the LT group than in the ECC group. The Fontan procedure of ECC has the advantages of avoiding aortic block and myocardial ischemia, shortening CPB time and maintaining a more streamlined inferior vena cava blood flow, and the superiority of long-term Fenestration has not been clarified.