In order to analyze the complicated water temperature distribution law in the intersection area and the influence mechanism of flow structure on it, the numerical simulation software Fluent was used to simulate the time-mean flow field, turbulence characteristics and water temperature distribution in the river junction area under different conditions by changing the confluence angle and the confluence ratio, and to analyze the relationship between the water temperature distribution characteristics (water temperature non-uniformity index) and the characteristic parameters of the flow structure (turbulence kinetic energy and vorticity) in the intersection area under different working conditions. The influence mechanism of different flow structure on the water temperature distribution was explored. The results show that the flow shear affects the position of the hot mixing layer and the secondary circulation affects the shape of the hot mixing layer. The larger the confluence angle or confluence ratio, the smaller the cross section non-uniformity index and the faster the water temperature mixing. With the change of shear layer location (turbulent kinetic quantization shear), the hot mixing layer is closer to the outer bank wall (intersection to side wall), and the bending degree of the hot mixing layer increases with the increase of secondary circulation strength. It shows a good linear relationship between turbulence kinetic energy and vorticity and section heterogeneity index.