Abstract Water-jet propulsions are widely used in high-performance ships. This study conducts numerical study on the unsteady flow of a complete water-jet propulsion. The internal flow field of the propulsion pump under the conditions of no installation of the shaft sleeve (and installation of the shaft sleeve. Spectrum analysis is used to compare the time-varying external characteristic and excitation characteristic under different conditions. Then, Dynamic Mode Decomposition technique is used to extract the high energy flow structures and corresponding frequencies. The results indicated that a large-scale vortex roll up above the driving shaft under the condition of rotational shaft, a pair of anti-rotation vortices appear behind the driving shaft under the condition of stationary shaft. These shaft induced vortices develop into unstable flow structures in the impeller region which moves relative to the impeller blades at rotational frequency. They further affect the unsteady flow in the guide vane region. The shedding vortices induced by the rotor-stator interaction are strengthened, while the passage vortices are weakened. Moreover, the dominant frequency of the passage vortex has decreased from 1.68 times the rotational frequency to 1.50 times the rotational frequency.