A 3-D viscous combined model adopting the large eddy simulation technology was developed, and employed in simulating the 3-D flow through a high head and high-rotation hydraulic turbine with the runner calculated in relative coordinate system and the draft tube computed in absolute coordinate system. The finite volume approach in space and the predictor-corrector method in time for the weakly compressible flow governing equations and a “tinny-slip" boundary condition for the solid wall were adopted, and the connected condition at the interface between the absolute coordinate system and the relative coordinate system was established. The pressure and velocity fields in the hydraulic turbine are simulated, which are consistent with the experimental results. Under partial load operating condition, especially, the separated flow and the negative pressure at the exit surface of the blade of the runner and a strong vortex in the cone and elbow section in the draft tube appear, even the back-flow near center line at entrance of the draft tube is in existence. The demonstration of the vortical band in the draft tube under partial load operating condition is successfully simulated, and its frequency is about one third of the rotating frequency of the runner, this vortical band is one of the main reasons for the vibration of the turbine generator unit.