Abstract: To study the characteristics of mixing and stratification in the Modaomen Estuary, a three-dimensional numerical salinity model was established based on SCHISM and then calibrated against measured data. Combined with the theory of the water potential difference, the temporal and spatial variation characteristics of mixing and stratification in the dry season and stratification mechanism of a deep channel and shoal were studied. The results show that water stratification is the strongest during the neap tide and is the weakest during the medium tide. Saltwater from the sandbar to Guadingjiao is always highly stratified. Along-channel advection, along-channel depth-mean straining and vertical mixing are the main factors that influence the water stratification of the deep channel. While cross-channel advection, cross-channel depth-mean straining and vertical mixing are the main factors that influence the water stratification of the shoal. In addition, there is a relatively high dissipation of turbulent kinetic energy (TKE) at the surface and bottom of the water column and low TKE dissipation at the middle of it. There is an asymmetric flood/ebb tidal distribution, with the flood higher than the ebb.