In medicine field, dynamic investigation of aorta artery has received attention due to its notable functions and significance upon performance of heart and individual health. Because, aortic injuries cause lethal occurrences having numerous mortality rates. Therefore, more probes, in particular, dynamic response of aorta arteries conveying blood flow containing pharmaceutical nanoparticles is essential. In present research, we attempt to model biomechanically the dynamic instability assessment of aorta arteries with atherosclerosis in tissue matrix conveying blood including pharmaceutical magnetic nanoparticles. Thus, according to classical cylindrical shell theory, the aorta arteries will be considered as elastic cylindrical vessels and symmetric lipid tissue is utilized in order to model atherosclerosis in the artery. Applying magnetic field to nanoparticles results in attraction of lipid tissue in artery. Moreover, the nature of blood flow is regarded non‐Newtonian based on Casson, Carreau, and power law models. Using Hamilton's principle, the motion equations are derived and based on differential quadrature method, the dynamic instability region of aorta artery is obtained. The influences of different variables such as magnetic field, magnetic nanoparticle's volume percent, combined effects of the tissue, lipid's height and length, and non‐Newtonian models upon dynamic behavior of aorta artery are investigated. According to the results, increase in lipid's height leads to increase in resonance frequency of aorta arteries.