The sensitivity of shear stress over smooth muscle cells (SMCs) to the deformability of media layer due to pressure is investigated in thoracic aorta wall using three-dimensional simulations. A biphasic, anisotropic model assuming the radius, thickness, and hydraulic conductivity of vessel wall as functions of transmural pressure is employed in numerical simulations. The leakage of interstitial fluid from intima to media layer is only possible through fenestral pores on the internal elastic lamina (IEL). The media layer is assumed a heterogeneous medium containing SMCs embedded in a porous extracellular matrix of elastin, proteoglycan, and collagen fibers. The applicable pressures for the deformation of media layer are varied from 0 to 180 mmHg. The SMCs are cylindrical objects of circular cross section at zero pressure. The cross sectional shape of SMCs changes from circle to ellipse as the media is compressed. The local shear stress over the nearest SMC to the IEL profoundly depends on pressure, SMCs configurations, and the corresponding distance to the IEL. The consideration of various SMC configurations, namely the staggered and square arrays, mimics various physiological conditions that can happen in positioning of an SMC. The results of our simulations show that even the second nearest SMCs to the IEL can significantly change their functions due to high shear stress levels. This is in contrast to earlier studies suggesting the highest vulnerability to shear stress for the innermost layer of SMCs at the intimal-medial interface.