Objective To evaluate the minimum effective dose of prostaglandin E1 (PGE1) in neonates with ductal-dependent congenital heart disease before interventional open cardiac surgery or open heart surgery.  Methods This study was retrospective 148 children with ductal-dependent congenial heart disease treated in our hospital were included. All children were at risk of worsening clinical symptoms because of  a significant cardiac defect after patient ductus arteriosus closure. The children were immediately injected with PGE1 at a dose of (0.003～0.010) μg/(kg·min) when their SaO₂＜75%. The does of PGE1 was then continuously and regularly measured and recorded, including start dose and minimum dose according to the degree of support of the arterial catheters to the pulmonary circulation and systemic circulation. The children were divided into two groups: the children with pulmonary blood flow insufficiency and/or heart and blood hypoventilation(group 1) and the children with systemic blood flow insufficiency(group 2). PGE1 dose and clinical characteristics were compared between the two groups. The children were divided into group A(complete transposition of the great arteries group), group B(pulmonory flow insufficiency group),group C(systemic flow insufficiency group)according to the shape of the ductus arteriosus.PGE1 does and clinical characteristics were compared between the tree groups. Spearman correlation analysis was used to assess the PGE1 -related factors. Results The minimal dose of PGE1 was (0.002～0.050) μg/(kg·min) and the average minimal dose was (0.0045±0.0004) μg/(kg·min) . PGE1 treatment time between the two groups were not statistically significant(P=0.968). The difference between the starting dose, and minimum dose of group 2 was statistically significant(P=0.022 and 0.007 maintenance dose respectively). The age of the children was positively correlated with the initial measurement of PGE1. There was a positive correlation between blood oxygen saturation and the start dose of PGE1 and the lowest dose of maintenance dose.  Conclusion Low-dose PGE1 can maintain the patency of catheter-dependent congenital heart disease. The children with systemic flow insufficiency need to have a higher dose of PGE1 compared with patients the children with complete transposition of the great arteries and pulmonary flow insufficiency group.