Coarctation of the aorta (CoA) is one of the most common congenital cardiac anomalies that could be corrected by surgery. However, the effects of surgical anastomosis on aortic arch flow are still unknown. In this study, a unique three-dimensional way was utilized to measure the growth of anastomotic site and computational fluid dynamics (CFD) was applied to investigate the hemodynamic effects of the growth of anastomosis site on patient-specific aortic arch flow before, 1 year and 2 years after surgery. The volume of anastomotic site, distribution of total pressure, wall shear stress (WSS), streamlines, energy efficiency and flow distribution ratio were calculated. The results indicated that the volume of anastomotic site has grown at 2-year follow-up. The total pressure and WSS were more uniformly distributed, whereas the three branches of aortic arch showed varying degrees of hypoperfusion. Energy efficiency increased obviously as the growth of anastomotic site. Our results implied that the numerical methods can be applied to evaluate the long-term effects of anastomosis site growth on aortic arch flow.