<p>The head-flow rate curve with double humps brings greater challenges to the stable operation of a pump-turbine in pump mode, and the present investigation aims to reveal the formation mechanisms behind it. We performed unsteady simulations by applying a modified partially averaged Navier-Stokes (PANS) model and the double hump phenomenon was satisfactorily captured with relative errors within 3.87% by comparing the head with the experimental data. The results showed that the rotating stall occurred in the guide vane during both the first and second hump regions and induced the dominant pressure pulsation component with an oscillating frequency 11.7% times the runner rotation frequency. The reverse flow was observed due to the propagation of rotating stall cells in the guide vane, and the first hump was attributed to the vortex in the vaneless region, with a reduction in the runner’s capacity for doing work as the reverse flow reached the blade trailing edge. The second hump was attributed to the flow separation near the leading edge of the runner blades, which extended to the runner outlet and interacted with the rotating stall cell, leading to a rapid extension of the reverse flow into the runner. This not only reduces the runner’s capacity for doing work but also significantly increases the energy loss in the blade-to-blade flow passage near the runner exit. This study enhances the understanding of the flow mechanism in the hump region, which can provide insights into the suppression of unstable flows and runner optimization.</p>