Atrial septal defect combined with interrupted inferior vena cava (IVC), which is a rare condition, makes it impossible to apply totally endoscopic surgery (TES). The most difficulty is how to drain blood from the posthepatic segment of the IVC. In this study, we report a case of a 44-year-old female patient who was diagnosed with secundum atrial septal defect combined with interrupted IVC with azygos–hemiazygos continuation. This patient underwent successful repair by TES with transthoracic cannulation for the posthepatic segment of the IVC.