The surgical treatment of congenital esophageal atresia is well established. Whether transthoracic or thoracoscopic-assisted, there have been more summary reports, but the surgical treatment of esophageal atresia combined with right-sided heart has not been reported. We have completed two such cases in succession and have the following experience. Regardless of the axillary incision or the posterior lateral incision, the right-sided heart occupies most of the space in the right “thoracic cavity”, and separating the pleura of the anterior chest wall and the mediastinal pleura allows the heart to sink to the left and facilitates the exposure of the posterior mediastinum. In one of the two patients, the esophagotracheal fistula was in a normal position, consistent with a common left-sided heart, with a slight posterior orientation. The other case was located on the left side of the trachea and required extensive freeing for complete exposure. The esophagotracheal fistula and the distal esophagus can be removed more smoothly by either expanding and contracting with respiration, or by upward evacuation from the diaphragm. In both right-sided children, the blind end of the proximal esophagus was left-sided and needed to be separated posterior to the trachea and superior posterior to the aorta to be exposed. Intraoperatively, the roving nurse or anesthesiologist was instructed to push the supporting gastric tube, and the blind end was seen to move, which was used to determine the general location of the superior blind end. During the separation, due to the proximity of the innominate vein and aorta, care was taken to operate carefully to prevent vascular injury. Preoperative upper gastrointestinal angiography was performed to clarify the diagnosis, and a right-sided heart was also found. The choice of surgical pathway was considered in advance accordingly. Although we successfully completed radical esophageal atresia through the right thoracic incision, it took significantly longer to expose the blind end of the proximal esophagus. In the second case, the preoperative upper gastrointestinal imaging showed that the proximal esophagus and esophagotracheal fistula were located on the left side of the trachea, which might be better exposed through the left thoracic incision. In addition, due to the artificial pneumothorax, the mediastinum was left-sided in the thoracoscopy, which might be more favorable for the exposure of the posterior mediastinum.