This paper deals with a robust shape control of a flexible structure against parameter variations. Based on a covariance control theory with the principle of detailed balance, a new linear state feedback control method is proposed, where the state vector is composed of the position, velocity, and integral variables. The robustness of the controlled system is acquired by approximate orthogonality between the eigenvectors of the system, and is confirmed with a condition number of the model matrix of the closed-loop system numerically. The usefulness of the proposed shape control method is also verified by hardware experiment.