Based on the generalized curvilinear coordinates system in plane and sigma coordinate system in vertical direction, a 3D flow numerical model is established. It adopts the control-volume formulation to disperse the basic equations. To avoid pressure oscillations, staggered grids are used. It uses the hydrodynamic pressure correction method to solve the equations. Then the model is validated respectively by the field data in classical sharp curve reach and in the Tugutang physical model. The results show that the proposed model can reasonably simulate 3D flow characteristics in the sharp curve reach, and flow condition in the entrance area of ship lock approach channel. It can be used to study and optimize the general layout scheme of hydro-junction.