Objective To study the risk factors for postoperative delirium (POD) in children with congenital heart disease. Methods A prospective nested case-control study was performed on children with congenital heart disease who underwent surgery in Fuwai Hospital, Chinese Academy of Medical Sciences, from December 2020 to June 2021. The clinical data were compared between the POD group (n=114) and non-POD group (n=102). A multivariate unconditional logistic regression analysis was used to investigate the risk factors for POD in children with congenital heart disease. Results The multivariate logistic regression analysis showed that age (OR=0.951, P<0.001), gender (OR=2.127, P=0.049), number of invasive catheters per day (OR=1.490, P=0.017), degree of postoperative pain (OR=5.856, P<0.001), and preoperative parental anxiety level (OR=1.025, P=0.010) were independent risk factors for POD in children with congenital heart disease. Conclusions The risk of POD increases in children with congenital heart disease who are younger, male, have higher number of invasive catheters per day, higher degree of postoperative pain, or higher preoperative parental anxiety level.