Abstract The stability of Francis turbine under low load conditions has become the focus in the power grid dominated by variable renewable energy. In this paper, the variable-speed approach is used to explore the operating characteristics of the Francis turbine, the RANS/LES hybrid turbulent model is adopted to investigate the fluid structure evolution process, and using the Q-criterion depicts the vortex cores. The results show that the numerical simulation agrees well with the experimental data acquired from the model test. It is found that the variable-speed operation can effectively eliminate the vortex ropes in the draft tube. Unexpectedly, the vortices in the runner will evolve from the separated vortices at the runner outlet for the fixed-speed Francis turbine to the inter-blade vortices at the runner inlet for the variable-speed Francis turbine in the case of small guide vane opening. It is concluded that the optimum operating range of a variable-speed Francis turbine (VSFT) should be within ±30% rated speed and 60% to 100% opening, and the pressure pulsation coefficient in the draft tube can be reduced from 7% to 1% at minimum water head, the output and efficiency of the turbine are increased by about 30% and 10% respectively.