Clotting of blood elements or intraluminal thrombus (ILT) is known to develop within aortic aneurysm sacs, and is clinically associated with the dilation and rupturing of aneurysms. However, the underlying factors that generate ILT are still unclear. We hypothesize that ILT can form under the influence of unfavorable hemodynamic patterns. This paper presents evidence for one such type of flow dynamics that could give rise to ILT within the aneurysm sac. Image-based patient-specific fluid–structure-interaction modeling of three cases of thoracic aortic aneurysms was performed, using retrospective CT images to investigate the formation of ILT as a result of local hemodynamic of aneurysm. This study showed that the formation of the ILT was associated with a vortex observed near the aortic narrowing, upstream of the aneurysm sac. This vortex could subject the blood elements to elevated stresses before directing them into the sac. The recirculation flow within the aneurysm sac may trap these activated blood elements, thus, leading to the formation of ILT during early diastole. One primary cause for ILT, as indicated in this study, could be attributed to the sharp curvature at the aortic narrowing (or isthmus) that gives rise to the vortex. Our study also showed that the size and location of the aneurysm have a direct impact on the duration and location of the vortex, which could influence the formation of the ILT.