The propulsion shafting whirling vibration causes non-uniform dynamic changes in the rotor tip clearance, which directly have a significant influence on the excitation force and vortex dynamic characteristics of the pump-jet propulsor. In the current study, based on improved delay detached eddy simulation, the influence of non-uniform blade tip clearance on the excitation force and vortex dynamics characteristics of the pump-jet propulsor is studied under design conditions. The results show that the application of propulsion shafting whirling vibration induces significant changes in the excitation force of the pump-jet propulsor. The rotor blades modulate the excitation forces of the stator blades and duct. The transverse and vertical excitation forces are more significant than the longitudinal excitation force. The magnitude change in the circular orbit shows a linear relationship with the excitation force magnitude. The characteristic frequency of the transverse and vertical excitation forces of each component is the shaft rotation frequency. In contrast, the characteristic frequency of the longitudinal excitation force is twice the shaft rotation frequency. In the elliptical orbit, the excitation force of each component is compressed or stretched in the time domain, and the dominant frequency is shifted in the frequency domain; there is no longer a linear relationship between the vibration magnitude change and the excitation force magnitude. Furthermore, an energy generation mechanism in the wake field of the pump-jet propulsor induces vortex frequency due to the whirling vibration of the propulsion shafting system.