As a key component of the ship propulsion device, the dynamic behavior of the marine rotor-bearing system under severe sea conditions is directly related to the stability and reliability of the propulsion device. The rotor-bearing system under ship heave motion was taken as the research object. Based on the long bearing theory and Lagrange equation, the dynamic model of the rotor-bearing system with parallel misalignment fault was established in the non-inertial reference system. The steady-state response of the system under various parameters was calculated and analyzed by numerical method, and the accuracy of the simulation results was verified by the rotor test bench. The results show that with the increase of the rotor speed, the axis orbit of the rotor system presents the characteristics of quasi-periodic motion and chaotic motion alternately. Heave motion aggravates the harmonic bifurcation phenomenon of the system and weakens the stability of the rotor to a certain extent. Especially in the low speed range, the influence of heave motion on the rotor system is particularly significant, while it is relatively weakened in the high speed range. In addition, the existence of parallel misalignment faults will significantly change the frequency components generated by the axis trajectory and heaving motion of the system in a specific direction of the rotor system.