An integrated structure and controller design approach for rotating cantilever beam is presented. An optimization method is developed for improving positioning performance considering the elastic deformations during high speed rotation and adopting the beam shape and the control gains as design variables. For this end, a dynamic model is setup by the finite element method according to the shape of the beam. The mass and stiffness of the beam are distributed in such a way that the closed-loop poles of the control system should be located leftmost in the complex s-plane. For optimization method, the simulated annealing method is employed which has higher probability to find the global minimum than the gradient-based down-hill methods. Sequential design and simultaneous design methods are proposed to obtain the optimal shape and controller. Simulations are performed with new designs by the two methods to verify the effectiveness of the approach and the results show that the settling time is improved for point-to-point position controls.