After the completion and operation of Quanzhou Bailai Water Control Project, the water supply capacity of Jinji sluice will be improved, resulting in the decrease of downstream water volume. In order to analyze the impact of the project on the estuary water environment, a two-dimensional unsteady water environment mathematical model of Jinjiang estuary is constructed by using MIKE21, and the tidal current field, salinity upstream distance, along-the-way change and diluted water area of the estuary before and after the construction of Bailai Reservoir are simulated. After analysis, the discharge of Jinji Gate is reduced by 53.4% at the maximum after the construction of the reservoir, and the prediction results show that the basic shape of tidal current field in Jinjiang estuary and coastal waters has not changed before and after the construction of the reservoir. The maximum increment of the upstream distance of the saltwater tide in Jinjiang Estuary is 0.66km, and the areas with obvious changes are mainly 2.6~12.3km in the upper reaches of Jinjiang Estuary, and the salinity variation is basically below 3.4‰. The area of diluted water in the experimental area of Quanzhou Bay Estuary Wetland Nature Reserve decreased by 3.4% at the maximum, but the core area and buffer area basically had no effect. Generally speaking, the Bailai Reservoir has little influence on tidal current field and salinity field in Jinjiang estuary after the reservoir is built. The research results can provide a basis for the protection and management of water environment in Jinjiang estuary, and can also provide some reference for the impact analysis of water environment in other estuary projects.