To achieve the flow mechanism during the closure of the guide vanes in a pump-turbine in pump mode, a three-dimensional (3-D) incompressible simulation using the shear stress transition (SST) k-ro turbulence model was performed. The dynamic mesh method was adopted to simulate the closing process of the guide vanes. Based on the validation of the steady experiments, the variation in performance characteristics (head, discharge, and torque), pressure, and velocity was presented, which shows dynamic instability at the end of the guide vanes closing process. Numerical results confirm that the dynamic instabilities at the end of the closing process originated from severe fluctuations that occurred in the guide and stay vanes. Detailed analyses of flow characteristics reveal that severe fluctuations occur due to vortices in the stay vanes, and a high-pressure circular ring in the vaneless space and a low-pressure circular ring between the guide vanes outlet and stay vanes inlet were identified. During the closing process of the guide vanes opening, the vortices appear in several passages initially, and then increasingly spread to all the passages. The position and rotating direction of the vortices vary with time. Using the Q-criterion method, the composition and evolution of vortex structures in stay vanes were identified. These structures comprise streamwise vortices, horseshoe-shaped vortices, and spanwise vortices, which lead to severe pressure fluctuations. (C) 2017 Elsevier Ltd. All rights reserved.