By taking the joint thin-walled parts as research object, a kind of research was carried out on the optimization of clamping scheme for the workpiece in milling process. The three-dimensional (3-D) model of fourflute end mill and the workpiece part were made by UG. The effect of different clamping scheme on the deformation of joint structure parts was simulated by the finite element analysis (FEA) software ABAQUS. With the purpose of getting the minimum of the average deformation, MATLAB genetic algorithm was based to optimize the clamping scheme and to acquire the best clamping scheme. The research results provide an effective method for controlling the deformation due to different clamping scheme of aeronautic joint-shaped workpiece.