Abstract: The large eddy simulation (LES) method base on a Vreman subgrid-scale model and the slide mesh technology of CFD were applied to accurately capture the flowing character in the Francis turbine passage under a small opening condition. Pressure distributions, velocity and vorticity as well as some special flow structures in guide vane near-wall zones and blade passages were gained. The results show that the tangential velocity component of fluid is dominant under a small opening condition. This situation aggravates the interactions between the wake vortices that shed from guide vanes. It leads to strong and complicated turbulent motion and all kinds of hydraulic instability phenomenon. There exists a pressure pulsation with a consistent low frequency, and main frequency energy in each flow passage parts from a spiral case to a runner computational domain, inducing the swirl vortex in a blade passage. Thusly, the non-uniform flow around a guide vane combined with the transmission of stress wave has a critical influence on the balance of a turbine and blade unit. In addition, the inter-Blade vortex is the main factor of blade fatigue failure.