Background: The high incidence of postoperative pulmonary venous obstruction (PVO) is a major mortality-associated concern in patients with right atrial isomerism and extracardiac total anomalous pulmonary venous connection (TAPVC). We evaluated new anatomical risk factors for reducing the space behind the heart after TAPVC repair. Methods: 18 patients who underwent TAPVC repair between 2014 and 2020 were enrolled. Sutureless technique was used in 12 patients and conventional repair in six patients. The angle between the line perpendicular to the vertebral body and that from the vertebral body to the apex was defined as the “vertebral-apex angle (V-A angle).” The ratio of post- and preoperative angles, indicating the apex’s lateral rotation, was compared between patients with and without PVO. Results: The median (interquartile range) age and body weight at repair were 102 (79-176) days and 3.8 (2.6-4.8) kg, respectively. The 1-year survival rate was 83% (median follow-up, 29 [11-36] months). PVO occurred in seven patients (39%), who showed an obstruction of one or two branches in the apex side. The postoperative V-A angle (46° [45°-50°] vs. 36° [29°-38°], P = 0.001) and the ratio of post- and preoperative V-A angles (1.27 [1.24-1.42] vs. 1.03 [0.98-1.07], P = 0.001) were significantly higher in the PVO group than in the non-PVO group. The cut-off values of the postoperative V-A angle and ratio were 41° and 1.17, respectively. Conclusions: A postoperative rotation of the heart apex into the ipsilateral thorax was a risk factor for branch PVO after TAPVC repair.