In this paper, the boundary control problem of a flexible rotatable manipulator in Three-Dimensional space with input constraints and actuator faults is taken into account. The Hamilton principle is introduced to derive the dynamic model represented by partial differential equations (PDEs), which can accurately reflect the characteristics of the distributed parameters of the flexible system. The hyperbolic tangent function is adopted to ensure that the control input is within a bounded range, and the projection-based adaptive laws are designed to estimate the degree of unknown actuator failures. Satisfying the input constraints, the system can still remain stable when the actuator failures ensue. The flexible manipulator can track the required angle, and both the elastic deformation and the deformation rate are effectively suppressed simultaneously. The numerical simulation results further illustrate the effectiveness of the proposed controller.