The finite element method based on fluid-structure interaction is used to systematically study the inertial migration of polymer vesicles in microtubule flow with a two-dimensional model, and the mechanism of the vesicles deformed by the fluid and the inertial migration phenomena are analyzed. The studies show that with the increase Reynolds number, the equilibrium position of vesicle inertial migration is farther and farther from its initial position; with the increase of blocking ratio, the equilibrium position of vesicle inertial migration is closer to the wall surface. For the modulus and viscosity of the vesicle membrane and for the membrane thickness, the results show that the modulus and viscosity determine the degree of deformation of the vesicle, and the modulus has little effect on the equilibrium position of the vesicle, but increases the viscosity, and the membrane thickness will promote the equilibrium position of the vesicle to be biased toward the center of the tube. This study helps to further clarify the deformation and equilibrium position of vesicles during inertial migration, and provides a reliable computational basis for the application of vesicles in drug transport, chemical reactions and physiological processes.