Abstract: To study the unstable operation mechanism of pump turbine induced by the frequent changes in the opening of the active guide vane, based on entropy generation theory and vorticity analysis, the method of combining numerical simulation and experimental tests was adoped to analyze the energy loss characteristics of pump turbine under three different working conditions of low flow, high efficiency and large flow. The research shows that with the increases in the opening of the active guide vane, the vortex value in the runner region increases, the entropy production in the high vortex value distribution region and the main flow region initially decreases and then increases, and the entropy production rate in the wall region increases. Variation law of energy loss is positively correlated with the variation law of flow disorder degree, and the vortex flow as well as impact, friction and other phenomena in the runner region are the important causes of energy loss. The experimental results of the same working condition model are similar to the numerical simulation results, which provides an important basis for the design and efficiency improvement of pump turbines.