Abstract: Concerning the complexity in flow characteristics and riverbed variations at the confluence region of natural river, a three-dimensional, numerical model of two phase flow is developed to explore the hydrodynamic characteristics of confluence flow between Yangtze River and Jialing River. The investigation focuses on the characteristics of separation zone, shear layer, flow velocity field, and helicity under the complex boundary and topography conditions. The results indicate that the pattern of separation zone is heavily influenced by the topography, tends to shift to the right-side of the river with the increasing of water level, and the shape of shear layer formulates a distorted, curved surface. Upon entering the confluence zone, all original secondary vortexes join together and present the tendency of moving to the right side of the channel; while the strength of the secondary flows tends to weaken on the right bank. In addition, two main helix flows are observed and captured at the confluence zone between Yangtze River and Jialing River.