With high velocity/acceleration and nanometer level motion accuracy requirements, the flexible dynamic behavior of ultraprecision wafer stage motion systems will significantly induce structural deformation, deteriorate control performance, and consequently, influence the final lithography accuracy. Inspired by this challenge, a new pole assignment control is proposed in this paper for multiinput–multiout (MIMO) systems with flexible structures. Specifically, through a closed-loop subspace identification and a modal approach, the modal state-space model is expressed as a diagonal subspace form that presents each rigid and flexible mode in these individual subspaces. Based on this model, a full-state feedback control architecture with a MIMO pole assignment control algorithm is developed to realize the modes’ control aims. The proposed control strategy is applied to a developed ultraprecision wafer stage. Comparative experiments were conducted on a single-input–single-output control, a MIMO control method with linear quadratic regulator control, and the proposed MIMO pole assignment algorithm. The results validate that the proposed scheme could achieve better disturbance rejection performance, transient performance, and excellent tracking accuracy in practical ultraprecision applications.