A typical three-dimensional flexible marine riser which is described by a distributed parameter system with several partial differential equations and ordinary differential equations is considered in this paper, we are aiming at limiting the top displacement of riser within restricted ranges. Appropriate boundary controls by integrating finite-dimensional backstepping technique with barrier Lyapunov functions are put forwarded to suppress the vibration of flexible riser under the external disturbance. The stability of the closed-loop system with the designed boundary control laws is proved by Lyapunov’s synthetic method without any discretization or simplification of the dynamic in the time and space when the initial conditions are satisfied. Furthermore, in order to illustrate the effectiveness of proposed controls laws, numerical simulation studies are carried.