The adaptive attitude control was examined for very flexible aircraft (VFA) with uncertainty. The high order of VFA model was reduced by a balanced realization approach, and the singular values of the original model and the reduced order model were investigated and compared. Based on the reduced order model, a LQR-PI controller was designed as baseline controller. Considering uncertainty, a model reference adaptive controller was designed by lyapunov stability theory and compared with LQR-PI controller. Simulation results show that the presented scheme has better control effect for VFA with uncertainty, and make the system perform desired attitude motion.