The impeller, which is the main energy conversion component of a pump as turbine (PAT), is designed for pumping mode, and its internal flow characteristics are quite complicated even at the best efficiency point (BEP) of the turbine mode. This study aims to investigate the flow separation characteristics in a PAT impeller under the BEP condition by numerical method. The hydraulic performance and transient pressure characteristics of PAT predicted numerically were verified through experimentation. The surface friction lines and flow topological structure were applied to diagnose the flow separation at the surface of the blade. The relationship between flow topological structure and vortex in the impeller and static pressure at the blade were analyzed. Analysis results show that the backflow and open flow separation are observed significantly in the leading region and near the shroud of the trailing region of suction side. The passage vortex always appears near the spiral node. The saddle point and spiral node correspond to the peak position of adverse pressure and the lowest position between two peak values of the static pressure of the blade, respectively. The inflow conditions of blade and shape of the trailing edge significantly influence the flow separations in the impeller.