In this article, boundary control strategy is adopted to suppress the vibration of a flexible three‐dimensional (3D) marine riser simultaneously against both sensor and actuator faults. The flexible 3D marine riser is a distributed parameter system modeled as partial differential equations. During normal operation of the system, all the system components will behave optimally. However, if the sensor and actuator appear fault, the system will work abnormally. While the sensor is faulty, the output signal of the sensor will have errors, and this error signal will be the input signal of the actuator. In terms of actuator fault, once the actuator appears fault problem, the actuator should make up for the fault and continue working for the sake of safety. In this work, the fault degree of sensors and actuators are unknown and the boundary control schemes using Nassbaum function are developed for fault compensation. The system stability is proven by introducing an appropriate Lyapunov function. Finally, the simulation results verify the accuracy of the proposed control laws.