Flexible structures are widespreadly applied in fields of aerospace. In order to obtain the best dynamic performance of the structures, the optimal locations of actuator and sensor become a key problem in active vibration control. The new proposed optimization criteria based on finite element dynamic equation ensuring good controllability or observability of the structures and considering the remaining modes effect were derived. Non-linear integer programming genetic algorithm was utilized to find the optimal positions of actuator and sensor. A cantilever plate was simulated by using state-feedback linear quadratic regulation controller to validate the vibration suppression effects. The comparison results of numerical simulation demonstrate the advantages of the proposed method.