The pump turbine is a crucial component of pumped storage hydropower plants. When operated at a constant speed, it does not respond well to variations in the grid frequency. To improve the hydraulic efficiency of pumped storage units, variable-speed units have been introduced. However, the mechanism of variable-speed pump turbines has not been extensively studied numerically. In this study, the flow characteristics of a variable-speed pump turbine were computed under two typical pumping modes, the maximum head and minimum flow rate condition, as well as the minimum head and maximum flow rate condition. The computed results aligned with experimental results, and the changing trends of hydraulic thrust under these two pumping modes were discussed. The error for the Hmax, Qmin condition was 1.3%, and the error for the Hmin, Qmax condition was −1.9%. These error values fell within a reasonable range. The research findings indicate that in the Hmax, Qmin condition, the flow within the flow passage exhibited higher velocity, which was 84.87 m/s, increased flow turbulence, larger pressure fluctuations, and poorer unit stability. On the other hand, in the Hmin, Qmax condition, both the axial hydraulic thrust and radial forces were greater, and there were sudden changes in the extreme values of pressure fluctuations over a certain period of time. It is recommended to avoid operating the variable-speed pump turbine under these two conditions during pumping operations.