In this paper, an adaptive multivariable continuous terminal sliding mode (CTSM) controller with robust input shaper (RIS) is proposed for flexible spacecraft under model uncertainty and external disturbance. Firstly, for the problem of flexible vibration introduced by flexible appendage, the RIS based on disturbance observer is designed. The proposed input shaper can eliminate the flexible vibration effectively even if there are some disturbances in flight. Then, an adaptive multivariable CTSM controller is proposed for attitude tracking of flexible spacecraft, using only information about the output and its first derivative. The features of the developed methods are that it is continuous multivariable controller which attenuates the chattering effectively and the attitude tracking can be achieved in finite time. The stability and robustness properties of the system are proven using Lyapunov function. Finally, some numerical simulations are performed to validate the efficiency of the developed algorithm.