A floating raft isolation structure is adopted to reduce the vibration of the marine rotor-bearing system, however, the system on the moving hull will be affected by the ship implicate motion, and its vibration will be difficult to predict. In this study, a dynamic model of the system under heaving and rolling coupled motion is established after considering the nonlinear oil film reaction force, unbalance inertia force, restoring force of the structure and inertia force of the ship motion. A numerical method is introduced to present the responses of the system, such as the amplitude and rotating speed curve, waterfall diagrams, and the rotor orbit and its Poincaré maps, etc. Moreover, the effects of rotating speed, amplitudes and frequencies of the coupled motion on the dynamic behaviours of the system are studied. The results indicate that the unstable region of rotating speed of the system increases under the coupled motion, the vibration of the system is greatly affected by the parameters of coupled motion, and the vibration amplitudes of rotor and raft can be effectively limited due to the displacement restrictor.