A rotating stall in centrifugal pumps commonly occurs under off-design operations, which is a detrimental phenomenon leading to flow instabilities, pressure fluctuations, and reduced performance. A time-resolved non-intrusive three-dimensional (3D) flow visualization method is developed for investigating complex vortex structures in centrifugal pumps based on Omega vortex identification and tomographic particle image velocimetry (tomo-PIV). A special-made centrifugal pump prototype was developed with acrylic glass allowing for optical access. This method enables both qualitative and quantitative analysis of high spatiotemporal resolution on flow behaviors and dynamics under various stall conditions. The ultra-high sampling frequency realized over 40 time-consecutive observations per revolution under 0.2 Qd, 0.4 Qd, 0.6 Qd, and 0.8 Qd. It captures the instantaneous evolution of vortex structures that undergoes a growth–breakup transition within 7–9 ms. The rotating stall mechanism is revealed experimentally from the evolution of the vortex structure. Our analysis shows the tomo-PIV's additional velocity component aids in understanding the 3D characteristics of the stall. A substantial region of reverse flow in the z-axis direction is observed under 0.2 Qd. Vortex structures are more prone to blockage at the impeller inlet, exacerbating the stall phenomenon. As the flow rate increases, the velocity distributions across different layers exhibit a laminar characteristic with a more uniform profile. The vortex structures extend radially and migrate toward the outlet. The evolutions of the stall vortex, wake vortex, and inlet vortex share the same dominant frequency components (4.75fn and 5.25fn), but the flow rate affects the proportion of different frequency components.