Understanding the formation mechanism of the S-shaped characteristics (SSCs) and the relationship between flow structures and the runaway instability (RI) is the prerequisite for optimizing runner design to promote operational reliability and flexibility. In this study, a new turbine equation is derived to reveal the prime cause of the SSCs, and the influence of geometric parameters on the SSCs is analyzed. Moreover, the flow patterns in three model turbines of different specific-speeds are simulated by unsteady Computational fluid dynamics (CFD), and the correlation between inverse flow vortex structures (IFVSs) and the RI in the SSCs region is identified. Theoretical analysis shows that the turbine equation can theoretically predict the change trend of the first quadrant SSCs curves of the pump-turbines; the flow losses caused by small blade inlet angle, instead of the diameter ratio, are the primary cause of the SSCs. The numerical simulation results reveal that the IFVSs at the hub side of the runner inlet are the origin of the RI; when operating points are far away from the best efficiency point (BEP), the IFVS locations change regularly. For large guide vane openings (GVOs), the IFVSs first incept at the shroud side, and then translate to the hub side, and further back to the midspan, when the discharge decreases. The inception points (IPs) of the SSCs correspond to the onset of the IFVSs at the hub side, which are in advance of the zero-torque operating points (ZTOPs); therefore, the ZTOPs are located in the positive slope region, leading to RI. For small GVOs, however, the IFVSs only locate at the midspan; the IPs of the SSCs, having no definite correlation with the IFVSs, are coincided with or are below the ZTOPs, because the ZTOPs are in the negative slope region and RI disappears. It is also found that the IPs of SSCs are the turning points of the predominant states between the turbine effect and pump effect. These results are valuable for design and optimization of pump-turbine runners.