Due to the influence of the rotating impeller in the water jet propulsion pump, the thrust generated by the water jet propulsion pump unit has a time-series pulsation characteristic. Firstly, through theoretical derivation, it is found that the thrust of a water jet propulsion pump unit is related to the outlet flow rate of the nozzle, and there is a pulsating characteristic of the thrust. Secondly, a direct thrust measurement system for the water jet propulsion pump unit was designed to achieve direct thrust measurement, further verifying the pulsating characteristics of thrust. The experimental results show that the transient thrust of the water jet propulsion pump unit fluctuates with time in a distinctly periodic manner, with low-frequency pulsations dominating. As the rotating speed increases, the amplitude of the subdominant frequency of the pump unit thrust pulsation tends to increase, while the influence of the impeller and guide vane on the transient thrust pulsation decreases with increasing speed, and the high energy density region in the wavelet transform time-frequency data gradually concentrates to the low-frequency. The experimental results and the related analysis can provide an empirical basis for studying the hydrodynamic aspects of the water jet pump unit.