The inter-blade passage vortex, the vortex rope of the draft tube, and the vortex in the guide apparatus are the characteristics of flow instability of the Francis turbine, which may lead to fatigue failure in serious cases. In the current study, in order to accurately capture the transient turbulent characteristics of flow under different conditions and fully understand the flow field and vortex structure, we conduct a simulation that adopts sliding grid technology and the large-eddy simulation (LES) method based on the wall-adapting local eddy viscosity (WALE) model. Using the pressure iso-surface method, the Q criterion, and the latest third-generation Liutex vortex identification method, this study analyzes and compares the inter-blade passage vortex, the vortex rope of the draft tube, and the outflow and vortex in the guide apparatus, focusing on the capture ability of flow field information by various vortex identification methods and the unique vortex structure under the condition of a small opening. The results indicate that the dependence of Liutex on the threshold is small, and the scale range of the flow direction vortex captured by Liutex is wider, but the ability of the spanwise vortex is relatively weak. The smaller the opening, the more disorderly the vortexes generated in each component and the more unstable the flow field. In the draft tube, the original shape of the vortex rope is destroyed due to the interaction between vortexes. Under the condition of a small opening, an inter-blade passage vortex is generated, affecting the efficient and stable operation of the turbine.