Recently, with the development of the marine economy, marine risers have garnered increasing attention as they present facile and reliable methods for oil and gas transportation. However, these risers are susceptible to vibrations, which can lead to system performance degradation and fatigue damage. Therefore, effective vibration control strategies are required to address this issue. In this study, a novel adaptive fault-tolerant control (FTC) strategy is adopted to suppress the vibrations of a 3-D riser-vessel system against the effects of actuator failures, backlash-like hysteresis, and external disturbances. A barrier-based Lyapunov function is merged to eliminate the time-varying output constraints of the system. Adaptive FTC laws with projection mapping operators are designed to compensate for parameter uncertainties and consider input nonlinearities to improve system robustness. Finally, a rigorous Lyapunov analysis and numerical simulations are performed to verify the validity of the proposed controller and guarantee uniformly bounded stability of the system.