Objective To evaluate the prevalence and potential risk factors of vitamin D deficiency in children with complex congenital heart disease. Methods A total of 138 children with complicated congenital heart disease undergoing improved Fontan operation were selected. The clinical data of the patients were analyzed retrospectively, including the basic population data, clinical characteristics and laboratory indexes of children. According to the international vitamin D nutrition status the seven-level classification,we assessed the incidence of vitamin D deficiency in children.We also analyzed the related factors that affect the level of vitamin D and parathyroid hormone. Results The average age of 138 children was(8.2±1.5)years.The average 25-hydroxyvitamin D level was(40.2±9.9）nmol/L.There were 100(72.5%)patients with vitamin D deficiency, 32(23.2%)cases of children with secondary hyperparathyroidism, 31(22.5%)cases of children with protein loss of gastrointestinal disease(PLG). Correlation analysis showed that serum 25-hydroxyvitamin D levels were positively correlated with calciumion levels(r=0.445, P=0.035); parathyroid hormone levels and granulocyte /lymphocyte ratios were positively correlated(r=0.495, P=0.037), and negatively correlated with lymphocyte count(r=-0.646, P=0.013);suggesting that there is a potential association between parathyroid hormone levels and inflammatory responses in children with complex congenital heart disease. Vitamin D deficiency in children with vitamin D supplementation, serum 25-hydroxy vitamin D levels were significantly increased in children with parathyroid hormone significantly reduced(P＜0.001). Conclusion The prevalence of vitamin D deficiency in children with complex congenital heart disease is high and is not associated with clinical features and laboratory indicators in children. There is a potentially important association between parathyroid hormone levels and systemic inflammatory responses.