The clocking positions between the inducer and the impeller have a certain impact on the performance of the high-speed centrifugal pump, which however, is often ignored by designers. In the present study, three-dimensional numerical simulation based on detached eddy simulation method is adopted to evaluate the influence of this clocking effect on unsteady pressure pulsations in a full-scale liquid rocket engine oxygen turbopump. A new omega vortex identification method is introduced to clarify the internal correlation between unsteady flow structures and pressure pulsations and to shed comprehensive light on the formation mechanism of this clocking effect. Results show that the clocking effect has little influence on the unsteady pressure field in inducer passages while it significantly affects the rotor–stator interaction (RSI) effect leading to the alteration of the pressure spectra in RSI region, diffuser and volute diffuser pipe. The components at the inducer blade passing frequency in the pressure spectra are remarkably suppressed and the total pressure pulsation energy in these regions is decreased by an average of 13.94%, 12.94%, and 34.65%, respectively, when the inducer blade trailing edges are located in the middle of two adjacent impeller blades. The vortex analysis in the specific region reveals that the pressure pulsations in RSI region and the downstream regions are closely associated with the unsteady vortex shedding from the diffuser blades and the formation of the clocking effect is precisely due to different processes of the periodic vortex shedding from the diffuser blade pressure surfaces.