Total anomalous pulmonary venous connection (TAPVC) is a rare congenital heart disease of newborns characterized by impaired left ventricle growth and diastolic dysfunction. We hypothesized that the patients with TAPVC reduced blood flow into the left heart prenatally could affect left atrium (LA) not just growth but function. We compared the age-related changes in LA deformation using two-dimensional speckle-tracking echocardiography (2DSTE) in Patients with TAPVC. This single-center, retrospective cohort study was conducted on consecutive isolated TAPVC patients who underwent neonatal surgery between January 1, 2009 and January 1, 2022. The LA datasets in TAPVC patients were analyzed before surgery (n = 28) and follow-ups at 1-2 (n = 24) and 5-7years of age (n = 13) and compared with those of age-matched healthy controls (January 2009-2022). The LA strain (ε), indicating LA function, was analyzed using QLAB represented by reservoir (εR), conduit (εCD), and contractile (εCT) strains. LA pressure was evaluated by periodic follow-up catheterization after repair. Compared to the controls, the TAPVC patients had significantly smaller LA maximum volume preoperatively, and with age, the LA maximal volumes reached normal levels, while the LA minimal volumes were larger. All 2DSTE-determined LA strains showed significant reductions at all time points in the TAPVC group compared to those in the control (median εR, εCD, and εCT; before surgery: 17.0% vs. 26.0%, 12.9% vs. 15.9%, and 6.3% vs. 10.4%; follow-up at 1-2years: 30.0% vs. 45.7%, 23.2% vs. 29.6%, and 6.1% vs. 16.3%; follow-up at 5-7years: 31.2% vs. 43.1%, 25.0% vs. 31.2%, and 5.2% vs. 10.8%, respectively; p < 0.05). Only εCT did not represented a significant change over time even though after correction of blood flow (median εCT: 6.0% → 5.9%). Patients with pulmonary venous obstruction (PVO) at birth showed significantly decreased εR and εCD and higher LA pressure compared to those without PVO. This study showed that nevertheless maximum volume of LA was recovered within the normal range, reduced LA strains, especially contractile function lasted from birth even after repair in Patients with TAPVC.