Abstract: In low-discharge operating conditions, serious vortices often appear in the runner blade channels of high-specific-speed Francis turbine runners. Transient dynamic stress of the runner has been numerically simulated and examined in this study to probe the mechanism of channel vortices acting on the blades and the cause of cracks on the runner. First, we calculated the steady and unsteady turbulent flows in the full passage based on the Navier-Stokes equations and a RNG k-ε turbulence model, and obtained the patterns and distributions of channel vortices that are very similar to experimental observations. Then, a finite element method was applied to modal analysis of the runner, showing the inherent frequencies and modal shapes. Finally, we adopted a fluid-structure coupling method to analyze the transient dynamics of the runner. Results show that the frequency of channel vortices acting on the blades is a multiple of the rotational frequency of runner and the most dangerous are the local channel vortices distributed near the joints of blade tailing edges with the crown. Thus, the maximum dynamic stress in the joints is higher than the allowable stress value of common turbine runners, leading to damage even cracks around that location.