Endovascular aneurysm repair (EVAR) is considered as a promising alternative technique for the treatment of aortic aneurysm. However, complications often occur after EVAR. In this paper, the influence of the physiological factors on the biomechanical behaviors of stented and non-stented thoracic aortic aneurysm (TAA) were presented. Representative TAA models with different intraluminal thrombus (ILT) volume before and after stent-graft (SG) implantation were built. Fluid-structure interaction effect was taken into account. The relative sliding between the SG wall and the aortic wall was allowed. Results showed that the cardiac cycle and ILT volume should be given much more consideration than previously thought in future investigations on TAA compliance. The time-averaged longitudinal displacement of SG necks were not uniformly distributed along circumferential direction of the aortic wall. Drag force increased with the increase of the cardiac cycle and decreased with the decrease of ILT volume. Computational results of TAA wall stress, sac and lumen pressure indicated that patient with faster heart rate might be at great risk of aneurysm rupture. The stress absorption effect of the SG was influenced by both ILT and cardiac cycle, which was also found to have strong impact on flow pattern. We believe that this study will bring new insights into further researches on the relevant issues and provide mechanics-based implications for clinical management of EVAR for TAA patient.