Objective To compare the early and mid-term results between Fontan operation and anatomic correction for congenitally corrected transposition of the great arteries (ccTGA). Methods The clinical data of 53 patients with ccTGA who underwent anatomic correction and Fontan operation from January 2009 to September 2021 in our hospital were reviewed, including 41 males and 12 females with a mean age of 55.02 (3-168) months. They were divided into an anatomic correction group (16 patients) and a Fontan operation group (37 patients) according to the operation. The hospitalization mortality, survival rate, postoperative complications, and free rate from re-intervention between the two groups were compared. Another 180 healthy children were recruited as a control group, and 14 children were matched with the propensity score matching method as a Fontan control group. The results of cardiopulmonary exercise testing (CPET) between the Fontan operation group and the Fontan control group were compared. Results There were 2 (12.5%) early deaths and 3 (18.8%) early re-intervention in the anatomic correction group, while 1 death and 2 re-intervention in the Fontan operation group. In addition, there were 9 patients (56.3%) in the anatomic correction group and 6 (16.2%) patients in the Fontan operation group suffering from arrhythmia after operation, respectively. Compared with the anatomic correction group, cardiopulmonary bypass time, aortic cross-clamping time, intubation time and ICU stay were significantly shortened in the Fontan operation group (P<0.05). CPET results showed that, percent predicted max VO2 in the Fontan operation group was lower than that in the Fontan control group (0.84±0.11 vs. 0.99±0.12, P＜0.05). The patients were followed up for 0.5-126.0 months. Two patients were lost in the Fontan operation group. There was no death and 1 re-intervention in the anatomic correction group, while no death or re-intervention in the Fontan operation group. The 1-year, 5-year and 10-year transplant-free survival rate of the anatomic correction group and the Fontan operation group was 87.5%, 87.5%, 87.5% and 97.3%, 97.3%, 97.3%, respectively (P＞0.05). The 48 patients were classified as grade Ⅰ-Ⅱ in cardiac function in the last follow-up. Conclusion There is no statistical difference in the transplant-free survival rate between the anatomic correction and the Fontan operation group. The postoperative complications in the Fontan operation group are decreased than those in the anatomic correction group. The Fontan operation is also a good choice, even though the patients with ccTGA meet the condition of the procedure of anatomic correction.