Studying the haemodynamics of the central shunt (CS) and modified Blalock-Taussig shunt (MBTS) benefits the improvement of postoperative recovery for patients with an aorta-pulmonary shunt. Shunt configurations, including CS and MBTS, are virtually reconstructed for infants A and B based on preoperative CT data, and three-dimensional models of A, 11 months after CS, and B, 8 months after MBTS, are reconstructed based on postoperative CT data. A series of parameters including energy loss, wall shear stress, and shunt ratio are computed from simulation to analyse the haemodynamics of CS and MBTS. Our results showed that the shunt ratio of the CS is approximately 30% higher than the MBTS and velocity distribution in the left pulmonary artery (LPA) and right pulmonary artery (RPA) was closer to a natural development in the CS than the MBTS. However, energy loss of the MBTS is lower, and the MBTS can provide more symmetric pulmonary artery (PA) flow than the CS. With the growth of infants A and B, the shunt ratio of infants was decreased, but maximum wall shear stress and the distribution region of high wall shear stress (WSS) were increased, which raises the probability of thrombosis. For infant A, the preoperative abnormal PA structure directly resulted in asymmetric growth of PA after operation, and the LPA/RPA ratio decreased from 0.49 to 0.25. Insufficient reserved length of the MBTS led to traction phenomena with the growth of infant B; on the one hand, it increased the eddy current, and on the other hand, it increased the flow resistance of anastomosis, promoting asymmetric PA flow.