For deep space probe subject to uncertain time-varying inertia matrix, unknown external disturbances, actuator faults, and misalignment, a fault-tolerant attitude controller is designed in this paper, which is based on adaptive control and fast terminal sliding mode control (FTSMC) theories. A new method to handle actuator uncertainties is developed, which redefines the effectiveness matrix and the misalignment matrix. Moreover, an explicit sufficient condition is presented in order to construct the fault-tolerant attitude controller. The proposed controller can stabilize the attitude control system with a fast convergence rate and high precision. Simulations results demonstrate the superior performance of the proposed controller.