The mouth bar is a common morphological unit in the river delta system. Its formation and evolution impose an impact on the material exchange between the estuary and ocean. Here we used an advanced wave-current coupled modeling system in an idealized estuary, with a prototype of the Modaomen estuary, China, to study the effects of the mouth bar on salt intrusion and the associated salt transport. The model results indicate that the mouth bar has a substantial effect on weakening the salt intrusion under the action of river discharge and tides, leading to a decrease in the salt intrusion length of 15～23%. When a down-estuary wind and a landward propagating offshore wave were included in the model, the mouth bar can decrease the salt intrusion length up to 21%. The hydraulic control at the mouth bar, in a state of partially blocked with lee jump, can enhance landward salt transport through tidal pumping. These findings indicate that the mouth bar has an important control on the salt transport, and provides implications for salt intrusion mitigation and sand resource management.