Abstract Purpose This study seeks to evaluate the impact of congenital heart disease (CHD) on somatic growth while controlling for the influence of other growth-related factors. Method A retrospective cohort study was conducted on identical twins, with one twin having CHD (CHD group) and the other without CHD (non-CHD group). Anthropometric measures, including weight-for-age (WAZ), height-for-age (HAZ), weight-for-height (WHZ), and head-circumference (HCZ) z-scores based on WHO growth standards, were employed, and growth failure was defined by z-scores below -2. Predictive factors of growth failure included gestational age, cyanosis, pulmonary arterial hypertension (PAH), heart failure, and ventricular physiology. Results Anthropometric indices from 41 pairs of twins were analyzed. The CHD group exhibited a significant decline in all growth parameters from the age of 1 year (p < .001). Although the growth disparity between twins lessened over time, the CHD group continued to lag behind the non-CHD group at follow-up (p < .05). Moreover, a higher proportion of the CHD group experienced malnutrition (46.3%) compared to the non-CHD group (7.5%, RR 1.724, 95% CI 1.280 to 2.232, p < .001, at the age of 1). Among disease characteristics, children with cyanosis, PAH, and heart failure displayed a significant decrease in growth z-scores compared to their unaffected twin siblings. However, statistical significance was observed only between weight-for-height z-scores and cyanosis (cyanosis 1.8±1.7 vs acyanosis -0.8±1.4, p = .032). Conclusion Children with CHD exhibited compromised growth compared to their non-affected twin siblings, with no complete catch-up growth observed during the observation period. The heightened prevalence of growth failure in the CHD group emphasizes the increased risk of malnutrition in children with CHD.