The confluence area serves as the pivotal control unit in natural rivers, and the implementation of spur dikes at the confluence enables regulation of flow patterns, influences pollutant mixing, and safeguards against river scouring. This study establishes a three-dimensional hydrodynamic model for the 90° confluence with dikes, aiming to explore the impact of the number, angle, and spacing of the dikes on hydrodynamic characteristics at 90° confluence. The results show that (i) the closer the spacing between the dikes, the wider the range of low water level area upstream becomes. An increased number of dikes makes it easier for the downstream water level to recover. (ii) The area of the high turbulent kinetic energy region increases with the increase in the number of dikes. Among the three angle deployments, the dike deployment angle of 60° corresponds to the largest area of high turbulent kinetic energy. When the spacing between dikes is 0.225 m, it results in the largest area of high turbulent kinetic energy. (iii) The number or spacing of dikes exhibits a negative correlation with the shape parameters of the separation and backflow behind the dikes, whereas there is a positive correlation between the angle of dikes and these shape parameters. (iv) Influenced by the deployment of dikes, novel helical flows will be generated around the dikes at the confluence. The helicity of the clockwise helical flow is comparatively smaller than that of its counterclockwise counterpart. Subsequently, newly generated helical flows undergo fusion and division as it progresses downstream.