To realize a multienergy complementary system involving hydropower and other energy sources, hydraulic turbines frequently run under partial flow conditions in which a unique flow phenomenon, the channel vortex, occurs in the runner, causing fatigue failure and even cavitation to the turbine blade. Cavitation severely shortens the service life of the unit and terribly limits the output of the turbine under partial flow conditions. In this paper, a numerical model of a Francis turbine was created with tetrahedral grids; the large eddy simulation (LES) method based on the WALE subgrid scale model and the Schnerr–Sauer cavitation model was adopted to carry out numerical simulation of the Francis turbine; and a vortex identification method based on the Q criterion was used to capture and analyze the channel vortex. The calculation results showed that a negative impact angle at the inlet of the runner occurred when the turbine ran under partial flow conditions, leading to three different types of channel vortexes in the blade channel. Also, different channel vortexes caused cavitation on different positions on the runner, and the volume change of cavitation showed periodic properties.