High-temperature superconductor has high critical temperature, high transport current capacity and low energy consumption, which correspondingly offer the wide applications in the field of electric power. As an important concern, the mechanical properties of superconductor carried with transport current have received extensive attention. Still, its mechanical properties in various electromagnetic environments are under study. Most of previous studies are based on the assumption of uniform distribution of critical current density, and only few researches based on the non-uniform distribution of critical current density are carried out. In this work, the mechanical flux pinning response of cylindrical superconducting structures is studied. Considering the non-uniform features of critical current density along the radial direction, the distribution law of induced magnetic field and current for the cylindrical superconducting structure is obtained based on the Bean model. Combined with the plane strain method, the analytical expression of magnetic flux pinning force, stress and magnetostriction in the superconducting structure are obtained. The results show that the uneven distribution of critical current density causes the flux pinning force to change, which further leads the superconductor`s local radial stress to vary with the critical current density. When the transport current flowing through the superconductor is increased in the ascending field, the radial stress and the hoop stress both appear compressive. The non-uniform distribution of critical current density has no significant effect on the overall trend of the internal stress, but displays an obvious influence on the stress distribution, and the superconducting structure is compressed and deformed. The results are consistent with those in the uniform case. When the transport current decreases during field descending, the critical current starts to reverse from the outermost part, then the compressive stress and tensile stress exist simultaneously. The hoop stress has a discontinuous point at the discontinuous portion of the critical current density, thus the damage probability is higher than that of the uniform distribution. In other words, the shear strength of superconductor is required to be higher for application. Also, the degree of magnetostriction is higher when the distribution of critical current density is set to be uniform, that is, the non-uniform distribution of the critical current density causes the superconducting structure to undergo greater deformation. Therefore, in engineering applications, the structural strength of the superconducting material must be enhanced to cope with the challenge from the uneven distribution of critical current density.