Abstract: Objectives The floating raft isolation system not only suppresses the low-frequency vibration transmitted by the pump-jet propulsor to the hull, but also causes low-frequency vibration in the vertical direction of the pump-jet propulsor. Studying on the unsteady forces caused by the dynamic changes of the tip-clearance is of great value for vibration reduction and noise reduction of pump-jet propulsors. Methods The overset grid is applied to construct a numerical model of SUBOFF with a pump-jet propulsor. Then the SST k-w turbulence model is used to calculate and analyze the working condition where the frequency of rotor vertical vibration is close to the rotor blade passing frequency. Results The result shows that the frequency and amplitude of the three-dimensional unsteady force of the rotor and the duct are both seriously affected by the dynamic changes of the tip-clearance. Conclusions The dynamic changes of the tip-clearance caused by the floating raft isolation system have a significant impact on the excitation source characteristics of the pump-jet propulsor. This study has guiding significance for the matching design between the floating raft isolation system and the pump-jet propulsor.