This article addresses the problem for vibration suppression of a multiple-sectioned marine riser system subject to time-varying external disturbances and asymmetric output constraint. Under the assumption that continuity constraint, multiple-sectioned marine riser’s dynamics are described by some continuously connected partial differential equations (PDEs) coupled with an ordinary differential equation (ODE). We only employ boundary control mechanism that suppresses system’s vibration displacements and compensate the influence of external disturbances. A novel and improved disturbance observer is proposed to estimate unknown boundary disturbance and two different barrier Lyapunov functions are constructed to prevent the time-varying constraint violation. Based on the backstepping technology and Lyapunov-based control, a boundary controller is presented to accomplish the control objectives. Moreover, the uniform boundedness and stability of the closed-loop system are rigorously guaranteed. Finally, simulation results are provided to illustrate the effectiveness of the designed control scheme.