Based on the FVCOM of the finite volume algorithm, a three-dimensional hydrodynamic-salinity-submerged dike coupling numerical model of the tidal river estuary was constructed by using the embankment treatment method under the unstructured grid. Taking the Minjiang River estuary as the research object, which is significantly affected by saltwater intrusion, the characteristics and laws of saltwater intrusion in the tidal reach of the Minjiang River under the influence of submerged dike construction were explored.The results demonstrate that the submerged dikes effectively suppress saltwater intrusion, with a more pronounced reduction in bottom-layer salinity than surface salinity and a stronger inhibitory effect during spring tides compared to neap tides.During spring and neap tides, the salt-suppressing effect of submerged dikes on shallow and wide channels with obvious water stratification is significantly better than that on narrow and deep channels with fully mixed water. During spring tide, the freshwater-saltwater interface in the North Channel retreated approximately 5 km and 8 km downstream due to the influence of Xia’nan and Jin’gangtui submerged dikes, respectively. Further analysis of water velocity and flow direction reveals that submerged dikes alter the flow velocity and direction of bottom water body, causing the bottom water flow to deflect while generating small-scale vortices, further suppressing the continuous upstream movement of saltwater.