In the present study, the internal flow field in a model pump-turbine operating in turbine mode was numerically studied. By recognizing that appearance of boundary vorticity flux (BVF)'s peaks might act as the precursors of flow separation in turbomachines, flow diagnosis based on the boundary vorticity dynamics was then performed. It was shown that the effect of the BVF distribution at the condition in design operating zone is to weaken the axial vorticity component omega(z), as well as to enhance the radial and circumferential vorticity components omega(z) and omega(theta). Thus, the peaks of the axial BVF component sigma(z) led to the strong weakening of omega(z), which is responsible for the flow separations. Geometric optimization for the runner was then achieved by modifying the inlet angle of the blade from 14 degrees to 16 degrees. The optimization successfully suppressed the occurrence of the flow separations and improved the moment on the runner at design operating condition by 4%, which was achieved by the redistribution of the axial BVF component generated by pressure sigma(pz) on the pressure side. The fact that only an accurate steady simulation is required for the analysis indicates the great potential application of this method in engineering practice. (C) 2020 Elsevier Ltd. All rights reserved.