Confluence River is a common occurrence in natural rivers, and the sediment transportation and pollutant dispersion strongly depend on the characteristics of flow structure in the confluence zone. Prior studies mainly focused on two dimensional properties of the separation zone, in which the variation of separation zone size from water surface to the bottom is often neglected. The experiments were performed in a flume, and the characteristics of separation zone were analyzed by the commonly used streamline and velocity isoline firstly proposed in this study. The velocity isoline method was conducted by the longitudinal velocity contour line for its big impact on flow structure. Based on the analysis of the selected data from prior experiments, the geometry and tendency of the separation zone may be changed with the variation of the different distance to the bottom and the discharge ratio between main and tributary rivers.