The problem of time-varying attitude tracking for a flexible satellite which is nonlinear in dynamics with moment-of-inertia uncertainty, flexible appendage dynamics, space disturbances and even the actuator faults is investigated in this paper. The quaternion description is adopted to formulate the kinematical representation, and the uncertain flexible satellite dynamics is described. Moreover, an adaptive updating law is proposed to estimate the upper boundary of the total uncertainty, which can guarantee the state variable of the closed-loop system to track the desired position. Furthermore, the fault detection and isolation (FDI) mechanism is not required to on-line diagnose the actuator faults in the proposed controller. Finally, numerical results are presented to verify the effectiveness of the proposed autonomous controller compared with two nominal sliding mode control schemes.