Background: Reversibility of pulmonary hypertension (PH) is closely related to the treatment options for and prognosis of children with congenital heart disease. Objective: We combined patient-specific clinical features including diagnosis, age and echocardiographic results, and biomarkers of pulmonary vascular dysfunction to explore the noninvasive methods that can be used to accurately evaluate the reversibility of pulmonary hypertension in congenital heart disease (PH-CHD). Methods: Based on the preoperative systolic pulmonary arterial pressure (sPAP), 70 CHD patients were divided into normal, PH-CHD suspected, and confirmed groups. Additionally, biomarkers of circulating endothelial cells (CECs), endothelin-1 (ET-1), and endothelial nitric oxide synthase (eNOS) were detected. Patients were categorized into reversible (RPH) and irreversible (IRPH) groups according to the sPAP 6 months after surgery. Risk stratification was performed according to the clinical features and biomarkers. Results: CECs and ET-1 levels in the confirmed group were significantly higher. eNOS was higher in the confirmed and suspected groups than that in the normal group. CECs in the IRPH group were significantly higher compared to the RPH group. No such intergroup differences were observed with respect to ET-1 and eNOS levels. The ROC curve showed that the risk stratification was of high diagnostic value to evaluate reversibility. Conclusion: The CECs, eNOS, and ET-1 were closely related with PH-CHD. CECs and risk stratification have high practical value in assessing the reversibility of PH-CHD.