Flow stability is extremely important for hydraulic turbines, especially for 1 GW hydraulic turbines, and has a strong impact on mesh stability. However, turbines often operate under non-design conditions, and current research on this aspect is still lacking. So a model of the fluid domains of a high-quality installed 1 GW Francis turbine was established to investigate the flow characteristics of the turbine and fluid domains. CFD simulations of a 1 GW Francis turbine under rated load and overload operation conditions were performed. According to simulation results, when the turbine is under the overload operation condition, the internal flow stability of the 1 GW hydraulic turbine can be obviously different from that of the rated load. In the overload condition, the flow field is more turbulent and a large number of vortices are generated in the draft tube, resulting in significant changes in pressure, flow rate, and output. In order to improve calculation accuracy, a pure clearance model containing only clearances and pressure balance pipes was established. The results of the full flow channel and pure clearance were compared. It was found that under the rated operating condition and the overload condition, compared with the pure clearance model, the axial force of the runner calculated by the full flow channel model is approximately 2−7% biased, the radial force is biased by approximately 7−8%, and the leakage flow is smaller.