The phenomenon that strong vibration of units occurred when the Francis turbine is operating under the small opening conditions, such as Gongzu, Shiquan, Liujia Gorges, Lijia Gorges and Three Gorges project. It was used the large eddy simulation (LES) method based on Vreman SubGrid Scale model to analysis the generation and evolution process of turbulence flow, captured the details of the flow structures and the dissipation of the turbulent kinetic energy. The SIMPIEC algorithm was applied to solve the coupled equation of velocity and pressure. The result shows that the small guide opening conditions deviated from the optimal conditions mostly. The unstable flow phenomenon including the swirl, flow separation, interruption and reflux was strong and complicated, which led to the abnormal vibration of the units.