Abstract: S-shaped curve is a widespread characteristic of pump-turbines, which has significant impact on unit operation. It is important to analyze underlying causes and control methods. This study has conducted numerical simulations of the whole passage of a model pump turbine and examined the characteristics of 3-D flow in the S-curve region for small guide vane opening, focusing on four different operating points to analyze the behaviour of internal flow in the unit. We found out that a large number of vortices appeared in the vane and runner sections at the points near runaway. The vaneless region between the guide vanes and runner was featured with an obvious water ring, where only a small amount of water was able to flow into the runner at the turbine braking point. In the reverse mode, the flow was very complicated. A comprehensive analysis of the 3-D flow reveals that in the S-curve region, a backflow in the vaneless region will block up all the channels if the unit operates in the condition of small discharge. This makes the runner unable to keep operating in the small discharge at a higher speed, and hence the S-shaped bend is created around the runaway point on the characteristic curve.