Flushing time of the Yangtze estuary by discharge is one of the important factors responsible for the transport of pollutants from various sources located along the Yangtze estuary: Therefore, an objective of the present study, which analysis flushing time in the case of different discharge is very helpful to evaluate the water environmental of the Yangtze estuary. Using a dissolved conservative material as a tracer in the water, a three-dimension advection-diffusion water exchange numerical model was used to study the flushing time by discharge and the discharge dominated region of the Yangtze estuary. The initial tracer concentration is set to 0.0 in the numerical domain of the Yangtze estuary, and the concentration value is set to 1.0 on the inflow boundary. The tracer flux normal to the solid boundary is set to 0.0. The flushing time and the out limit of discharge dominated region can be calculated in terms of the tracer concentration. Estuarine, Coastal and Ocean Model (ECOM) is used as the hydrodynamic model. The result shows that the flushing time is approximately in inverse proportion to the discharge at the upper stream. The out limit is farther from the upper inflow boundary as discharge increases. The out limit at the north branch is different from that of the south branch because the discharge into the north branch is much less than that into the south branch. The data is qualitative similar to the observed data, which show the three-dimensional advection-diffusion equation can be used to estimate the flushing time and the discharge dominated region of the Yangtze estuary. Flushing time of the Yangtze estuary by discharge is one of the important factors responsible for the transport of pollutants from various sources located along the Yangtze estuary: Therefore, an objective of the present study, which analysis flushing time in the case of different discharge is very helpful to evaluate the water environmental of the Yangtze estuary. Using a dissolved conservative material as a tracer in the water, a three-dimension advection-diffusion water exchange numerical model was used to study the flushing time by discharge and the discharge dominated region of the The initial tracer concentration is set to 0.0 in the numerical domain of the Yangtze estuary, and the concentration value is set to 1.0 on the inflow boundary. The tracer flux normal to the solid boundary is set to 0.0. The flushing time and the out limit of the dominated region can be calculated in terms of the tracer concentration. Estuarine, Coastal and Ocean Model (ECOM) is u sed as the hydrodynamic model. The out shows that the flushing time is approximately in inverse proportion to the discharge at the upper stream. The out limit is farther from the upper inflow boundary as discharge increases. The out limit at the north branch is different from that of the south branch because the discharge into the north branch is much less than that into the south branch. The data is derived similar to the observed data, which show the three-dimensional advection-diffusion equation can be used to estimate the flushing time and the discharge dominated region of the Yangtze estuary.