Objective To analyse the risk factors for the early failure of systemic-to-pulmonary artery shunt in cyanotic congenital heart disease (CHD). Methods The clinical data of 73 patients with cyanotic CHD undergoing systemic-to-pulmonary artery shunt were retrospectively analysed. The perioperative objective parameters were collected. Univariant analysis was performed with Chi-square test and multivariate analysis was carried out with Logistic regression analysis to seek the risk factors for early failure after systemic-to-pulmonary artery shunt. Results Fourteen patients experienced early failure. Chi-square test indicated that pulmonary atresia/intact ventricular septum, age no more than 60 d, long time of cardiopulmonary bypass, pulmonary artery enlargement and higher maximal inotrope score (ISmax>20) after surgery were associated with early failure. Logistic regression analysis revealed that pulmonary artery enlargement and ISmax>20 after surgery were independent risk factors for early failure. Conclusion For patients with cyanotic CHD having risk factors for early failure after systemic-to-pulmonary artery shunt, the management of intensive care after systemic-to-pulmonary artery shunt should be enhanced to reduce the incidence of early failure.