Objective This study aimed to determine the longitudinal change of systemic ventricular function and atrioventricular valve regurgitation after total cavopulmonary connection. Methods In 620 patients who underwent total cavopulmonary connection between 1994 and 2021, 4219 longitudinal echocardiographic examinations of systemic ventricular function and atrioventricular valve regurgitation were evaluated retrospectively. Results The most frequent primary diagnosis was hypoplastic left heart syndrome in 172, followed by single ventricle in 131, tricuspid atresia in 95, and double inlet left ventricle in 91 patients. Dominant right ventricle was observed in 329 (53%) and dominant left ventricle in 291 (47%). Median age at total cavopulmonary connection was 2.3 (1.8–3.4) years. Transplant-free survival at 5, 10, and 15 years after total cavopulmonary connection was 96.3, 94.7, and 93.6%, respectively in patients with dominant right ventricle and 97.3, 94.6, and 94.6%, respectively in those with dominant left ventricle (p = 0.987). Longitudinal analysis of systemic ventricular function was similar in both groups during the first 10 years postoperatively. Thereafter, systemic ventricular function worsened significantly in patients with dominant right ventricle, compared with those with dominant left ventricle (15 years: p = 0.007, 20 years: p = 0.03). Atrioventricular valve regurgitation was more frequent after total cavopulmonary connection in patients with dominant right ventricle compared with those with dominant left ventricle (p < 0.001 at 3 months, 3 years, 5 years, 10 years, and 15 years, p = 0.023 at 20 years). There was a significant correlation between postoperative systemic ventricular dysfunction and atrioventricular valve regurgitation (p < 0.001). Conclusions There was no transplant-free survival difference and no difference in ventricular function between dominant right ventricle and dominant left ventricle for the first 10 years after total cavopulmonary connection. Thereafter, ventricular function in dominant right ventricle was inferior to that in dominant left ventricle. The degree of atrioventricular valve regurgitation was significantly higher in dominant right ventricle, compared with dominant left ventricle, and it was positively associated with ventricular dysfunction, especially in dominant right ventricle.