Objective To investigate the iron deficiency (ID) in children with congenital heart disease (CHD) and find high risk factors of ID. Methods The clinical data of 227 pediatric patients with CHD from February to June 2016 were retrospectively analyzed. The incidence of ID according to the result of iron metabolism examination (serum ferritin <12 μg/L as the diagnostic criteria) was investigated. According to their basic CHD types, patients were divided into a cyanotic group and an acyanotic group. We tried to find the high risk factors of ID in those pediatric CHD patients by comparing their age, gender, growth condition and blood routine test results. Results There were 19.8% pediatric CHD patients complicated by ID. The incidence of ID in the cyanotic patients was higher than that in the acyanotic patients (31.0% vs. 17.3%, P=0.045). In both groups, ID patients presented the characteristics of younger age, higher anemia rate, lower mean corpuscular volume (MCV), lower mean corpuscular hemoglobin (MCH), lower mean corpuscular-hemoglobin concentration (MCHC) and longer red blood cell distribution width (RDW). Conclusion Cyanosis, younger age (infant), anemia, decreased MCV, decreased MCH, decreased MCHC and increased RDW are high risk factors of ID in CHD children.