An improved eigenstructure assignment algorithm with output feedback is presented to solve the problem that the general eigenstructure assignment with output feedback can’t completely guarantee the stability of the closed-loop system. In this improved algorithm, the quadratic performance index is introduced to convert the problem of the closed-loop stability into a linear quadratic optimal control problem, which ensures the stability of the closed-loop system. Taking into account that the closed-loop system designed by eigenstructure assignment has a poor robustness, the condition for ensuring the system robustness is given to solve the robust problem of the closed-loop system. Finally, simulation results on a flying wing aircraft show the effectiveness of the eigenstructure assignment proposed.