Abstract: To solve the problem of the shape optimization of holed structure, a method that integrates extended isogeometric analysis and a chaotic ion motion algorithm is proposed. For mechanical calculations of holed structure, extended isogeometric analysis is used to divide the background meshes in geometric shape, and to describe the boundary of the holes with non-uniform rational B-splines where there is no integral in the area of the holes in the assembly of the stiffness matrix. In addition, to obtain high precision integral calculations, refinement by the adaptive four-forked tree is performed in the element related to the hole boundary. In the optimization model, the control points for describing the structure are set to be the design variables, and the optimization objective is to minimize the mass of the structure. The optimization model is then solved by using the ion motion optimization algorithm instead of the traditional asymptotic method based on sensitivity analysis. The calculation results of the infinite plate with a circular hole by extended isogeometric analysis and the optimization result of a torque arm structure proved the validity of this method.