This study presents the numerical analysis on the inter-blade vortex characteristics along with the blockage effects of runner blade in a Francis hydro turbine model with various flow rate conditions. The turbine model showed different flow characteristics in the runner blade passages according to operating conditions, and inter-blade vortex was observed at lower flow rate conditions. This inter-blade vortex can lead to performance reduction, vibration, and instability for smooth operation of turbine systems. The previous study on blockage effects on various runner blade thickness, showed its influence on hydraulic performance and internal flow characteristics at low flow rate conditions. Therefore, the inter-blade vortex characteristics can be altered with the blockage effects at low flow rate conditions in a Francis hydro-turbine. For investigating the internal flow and unsteady pressure characteristics, three-dimensional steady and unsteady Reynolds-averaged Navier-Stokes calculations are performed. These inter-blade vortices were captured at the leading and trailing edges close to the runner hub. These vortex regions showed flow separation and stagnation flow while blockage effects contributed for decreasing the inter-blade vortex at low flow rate conditions.