<p>Operation of pump-turbines in the S-shaped region is characterized by amplified pressure pulsations and grid synchronization challenges, often leading to operational instability and compromised grid compatibility. This study employs dynamic mode decomposition (DMD) method to extract coherent flow structures correlated with dominant pressure pulsation frequencies in the S-shaped region, while experiments have been conducted to validate numerical simulations. Results show that the DMD method can effectively identify characteristic frequencies of complex flows in the S-shaped region: low-frequency pressure pulsations in the vaneless space originate from circumferential transmission component of the water ring over time, which is called the water ring pulsation component. During operation condition transitions, this pulsation component first intensify then attenuate as it moves outward along the guide vanes. The dominant draft tube pressure pulsation frequency driven by vortex rope dynamics induces morphological vortex rope transformations via DMD mode shifts during operational transitions. Runner pressure pulsations within the S-shaped region predominantly stem from rotating stall propagating counter to the runner’s rotation. These findings advance the understanding of S-shaped region flow instabilities, linking component-specific flow structures to global pressure pulsation characteristics, and thereby providing critical insights for operational stability enhancement.</p>