Objective Hemodynamic disorder of the pulmonary artery (PA) is the main cause of pulmonary arterial hypertension related to congenital heart disease (PAH-CHD). To study the hemodynamic characteristics of PA, so as to understand biomechanical factors in the occurrence and development of PAH-CHD. Methods Clinical and imaging data were collected in five PAH-CHD patients and five matched controls (Non-PAH) to reconstruct subject-specific three-dimensional (3D) PA models. Computational fluid dynamics (CFD) was performed to compare the hemodynamic difference of flow patterns, wall shear stress (WSS) and normalized energy loss (E·) in the two groups. Results Hemodynamics-related parameters showed that the velocity and WSS were higher in the left and right PA branches of PAH-CHD patients, with significantly lower WSS in the main PA. The E· significantly increased in PAH-CHD patients and positively correlated with normalized PA diameter and inflow. Conclusions Compared with Non-PAH subjects, PAH-CHD patients have obviously higher velocity and WSS in PA branches, lower WSS in main PA and greater E·, indicating these hemodynamic parameters are related with the PAH-CHD, which can be used as potential biomechanical factors for the clinical evaluation of PAH-CHD.