This study aimed to explore anatomical and hemodynamic features of atrial septal defect, which was treated by transcatheter device closure late after completion of biventricular circulation in patients with pulmonary atresia and intact ventricular septum (PAIVS) or critical pulmonary stenosis (CPS). We studied echocardiographic and cardiac catheterization data, including defect size, retroaortic rim length, single or multiple defects, the presence of malalignment atrial septum, tricuspid and pulmonary valve diameters, and cardiac chamber sizes, in patients with PAIVS/CPS who underwent transcatheter closure of atrial septal defect (TCASD), and compared to control subjects. A total of 173 patients with atrial septal defect, including 8 patients with PAIVS/CPS, underwent TCASD. Age and weight at TCASD were 17.3 ± 18.3 years and 36.6 ± 13.9 kg, respectively. There was no significant difference in defect size (13.7 ± 4.0 vs. 15.6 ± 5.2 mm, p = 0.317) and the retro-aortic rim length (3.7 ± 4.3 vs. 3.6 ± 0.3.1 mm, p = 0.948) between the groups; however, multiple defects (50% vs. 5%, p < 0.001) and malalignment atrial septum (62% vs. 14%. p < 0.001) were significantly frequent in patients with PAIVS/CPS compared to control subjects. The ratio of pulmonary to systemic blood flow in patients with PAIVS/CPS was significantly lower than that in the control patients (1.2 ± 0.4 vs. 2.0 ± 0.7, p < 0.001); however, four out of eight patients with atrial septal defect associated with PAIVS/CPS had right-to-left shunt through a defect, who were evaluated by the balloon occlusion test before TCASD. The indexed right atrial and ventricular areas, the right ventricular systolic pressure, and mean pulmonary arterial pressure did not differ between the groups. After TCASD, the right ventricular end-diastolic area remained unchanged in patients with PAIVS/CPS, whereas it significantly decreased in control subjects. Atrial septal defect associated with PAIVS/CPS had more complex anatomy, which would be a risk for device closure. Hemodynamics should be individually evaluated to determine the indication for TCASD because PAIVS/CPS encompassed anatomical heterogeneity of the entire right heart.