Background: The associated factors of malnutrition in children with congenital heart disease (CHD) must be evaluated to provide evidence for the treatment and care of such children. Methods: Two investigators searched the PubMed database until 25 June 2023 for literature about the associated factors of malnutrition in children with CHD. A meta-analysis of associated factors of malnutrition was performed by RevMan 5.3 software. Results: Thirteen studies involving 8,031 children with CHD were included. Pulmonary hypertension (OR = 3.81, 95% CI: 2.46-4.12), low birth weight (OR = 2.69, 95% CI: 1.25-5.77) and parents' height (OR = 2.15, 95% CI: 1.89-2.92) were the associated factors of growth retardation (all P < 0.05). Pulmonary hypertension (OR = 3.77, 95% CI: 3.13-4.24), low birth weight (OR = 3.04, 95% CI: 2.61-4.18) and pneumonia (OR = 2.35, 95% CI: 2.08-2.83) were the associated factors of low body weight of children with CHD (all P < 0.05). Conclusions: Medical staff should fully understand the risk factors, strengthen nutritional support and enhance nursing care for children with CHD to reduce malnutrition.