Postoperative arrhythmias are common in pediatric patients undergoing cardiopulmonary bypass (CPB); however, their impact on long-term cardiac function remains unclear. To investigate the association between postoperative arrhythmias and long-term cardiac function, and to develop a prediction model for adverse outcomes. This retrospective cohort study included 712 children with congenital heart disease who underwent CPB. Postoperative arrhythmias were assessed using continuous electrocardiographic monitoring. The primary outcome was impaired long-term cardiac function at 6-12 months postoperatively. Multivariable logistic regression and least absolute shrinkage and selection operator (LASSO) regression were used to identify associated factors. The incidence of postoperative arrhythmias was 40.6%. Prolonged corrected QT (QTc) interval and premature ventricular contractions (PVCs) were significantly associated with impaired long-term cardiac function. A dose-response relationship was observed between the number of postoperative arrhythmia types and the risk of adverse outcomes (P for trend < 0.001). Multivariable analysis identified CPB duration (odds ratio [OR] = 1.02), QTc prolongation (OR = 2.70), and PVCs (OR = 1.88) as independently associated factors. The prediction model demonstrated moderate discriminative ability (area under the curve [AUC] = 0.67) and provided a certain degree of clinical net benefit. Risk stratification analysis revealed a clear gradient in the incidence of adverse outcomes across risk groups (6.3% vs 12.3% vs 21.8%).  Conclusions: Postoperative arrhythmias, particularly QTc prolongation and PVCs, are closely associated with impaired long-term cardiac function. The developed prediction model enables effective risk stratification and may facilitate individualized postoperative management.