Background: Low cardiac output syndrome (LCOS) is an important complication of cardiac surgery. It is associated with increased morbidity and mortality. The incidence of LCOS after surgery is high in patients with congenital heart disease (CHD). Therefore, determining the risk factors of LCOS has clinical significance for the management of CHD. This study aimed to analyze the risk factors of LCOS. Methods: We conducted a retrospective analysis of children with CHD who underwent cardiac surgery at Shanghai Children's Medical Center between January 1, 2014, and December 31, 2017. Demographic characteristics and baseline data were extracted from the health data resource center of the hospital, which integrates clinical routine data including medical records, diagnoses, orders, surgeries, laboratory tests, imaging, nursing, and other subsystems. Logistic regressions were performed to analyze the risk factors of LCOS. Results: Overall, 8660 infants with CHD were included, and 864 (9.98%) had LCOS after surgery. The multivariate regression analysis identified that age (OR 0.992, 95% CI: 0.988-0.997, p = 0.001), tricuspid regurgitation (1.192, 1.072-1.326, p = 0.001), Risk Adjustment in Congenital Heart Surgery-1 risk grade (1.166, 1.011-1.345, p = 0.035), aortic shunt (left-to-right: 1.37, 1.005-1.867, p = 0.046; bi-directional: 1.716, 1.138-2.587, p = 0.01), atrial shunt (left-toright: 1.407, 1.097-1.805, p = 0.007; right-to-left: 3.168, 1.944-5.163, p < 0.001; bi-directional: 1.87, 1.389-2.519, p < 0.001), ventricular level shunt (left-to-right: 0.676, 0.486-0.94, p = 0.02; bi-directional: 2.09, 1.611-2.712, p < 0.001), residual shunt (3.489, 1.502-8.105, p = 0.004), left ventricular outflow tract obstruction (3.934, 1.673-9.254, p = 0.002), right ventricular outflow tract obstruction (3.638, 1.225-10.798, p = 0.02), circulating temperature (mild hypothermia: 1.526, 95% CI: 1.205-1.934, p < 0.001; middle and low temperature: 1.738, 1.236-2.443, p = 0.001), duration of cardiopulmonary bypass (1.009, 1.006-1.012, p < 0.001), myocardial preservation using histidine-tryptophanketoglutarate (1.677, 1.298-2.167, p < 0.001), and mitral insufficiency (1.714, 1.239-2.37, p < 0.001) were independent risk predictors of LCOS. Conclusions: The incidence of postoperative LCOS in CHD children remains high. Circulation temperature, myocardial preservation using histidine-tryptophan-ketoglutarate, and usage of residual shunt after surgery were independent risk predictors for LCOS.