In the pump mode (storage mode) of a pump-turbine, unstable head variations occur as the flow rate decreases, leading to unstable, unsafe operation. Thus, the hydrodynamics of pump-turbines in the unstable operating range should be investigated to improve their designs. This study presents experimental and numerical studies of the hydrodynamics. The experiments investigated the external characteristics with the head instabilities captured by both the model tests and the computational fluid dynamics simulations. The computational fluid dynamics model used detached eddy simulations to study the flow details which showed that hydraulic losses were the reason for the unstable head variations and the poor flow regime was the source of the losses. In the unstable, low flow rate range, the flow direction is no longer consistent with the guide vane direction, so undesirable flow structures develop in the passages. Therefore, appropriate guide vane opening angles are needed to improve the flow regime and reduce the hydraulic losses. These will enhance the operating stability and safety in engineering applications.