Abstract: Stratification effect is a typical feature in natural estuarine. This paper uses TELEMAC three-dimensional hydrodynamic mathematical model to study the transport and diffusion laws of thermal effluent in an idealized estuary under different stratification intensities. The results show that: the neap tide with the largest stratification intensity, the vertical diffusion of thermal effluent is significantly restrained, resulting in the middle layer with a significantly higher temperature and its envelope area than that of the surface and bottom layer, the strong gravity circulation during neap tide leads to a net upstream distribution trend of temperature envelope range in the middle and lower layers; the spring tide with the weakest stratification intensity but the largest tidal mixing effect has the smallest overall influence range of thermal effluent; the temperature envelope distribution under mid-tide conditions is similar to that of the neap tide, but the influence range is reduced. The calculation results of the mid-tide without considering stratification show that the influence range of thermal effluent in surface layer is significantly higher than that of other layers, the influence range of thermal effluent below the middle layer is very small, and there is no net distribution trend to the upstream. It can be seen that in stratified estuary, the transport and diffusion laws of thermal effluent are significantly different from those in non-stratified water bodies. Therefore, the influence of stratification effect should be considered during the design of water intake and drainage.