In this study, the quasi-3D model composed of depth-integral vortex equation and shallow water equations was extended on the basis of finite volume method employing non-orthogonal grids for properly evaluating complex boundary of the confluences. And, we developed the flux integral method considering non-orthogonal direction of grid line based on the CIP-CSL scheme for evaluating the convection terms more accurately also in the complex flow field of the confluence. The extended quasi-3D model was applied to recent large floods at the Go River confluences to investigate the flood flow and bed variation during the flood events. From the calculation results, we clarified that separation zones formed at the confluences have pronounced effects on the three dimensional flow structure and bed variations for the downstream channel.