To reveal the causes of efficiency degradation in a large Francis turbine under high-load conditions, a numerical simulation investigation was conducted on the mechanism of vortex-induced energy losses. The mean kinetic energy theory was employed to quantify hydraulic losses in each flow passage component, while the rigid vorticity theory was adopted to identify complex vortex structures in the runner and draft tube. The results show that once the discharge exceeds the rated value, the runner and draft tube become the dominant sources of hydraulic loss, accounting for up to 30% and 75% of the total hydraulic loss, respectively. The flow separation-induced vortex at the leading edge of the runner blade merges with the horseshoe vortex at the blade root, producing intense shear flow and significantly increasing energy loss near the leading edge. The velocity gradient between the low-velocity flow near the vortex core of the cylindrical vortex rope in the draft tube and the high-velocity main flow in the outer region significantly enhances turbulent kinetic energy dissipation. The separation vortex in the runner and the cylindrical vortex rope in the draft tube are the primary loss sources under high-load conditions. Their intensities increase with discharge, leading to a substantial reduction in turbine efficiency.