When sudden pollution accidents occur in temperature stratified reservoirs， it is of great significance to grasp the hydrodynamic and water temperature characteristics of water bodies to judge the development of pollution events and guide policy-making. MIKE3 software can be used for the three-dimensional simulation of reservoir hydrodynamics and water temperature. In order to explore further the influence of the model’s horizontal grid division and vertical coordinate system selection on the density flow， based on previous physical model experiments the numerical models of triangular， rectangular， and triangular-rectangular coupled grids are constructed. The σ coordinates and σ-Z mixed coordinates are adopted. The results show that MIKE3 software can effectively simulate the characteristics of temperature stratified density flow. It can be concluded that when the mainstream direction of density flow is very significant， it is recommended to use a rectangular grid to discretize the study area. The ladder approximation of Z-coordinate model can be effectively weakened by increasing the number of vertical stratifications. For water bodies with large differences in temperature stratifies interface， mainstream direction and the slope of riverbed， it is recommended to use σ-Z mixed coordinates in the vertical direction.