A three-dimensional semi-implicit finite volume numerical model has been developed and applied to study tidal circulation and salinity stratification in the region of Oujiang River Estuary, China. The model employs horizontally unstructured grids and boundary-fitted coordinate system in the vertical direction. Governing equations consisting of continuity, momentum, and transport equations are all solved in the integral form of the equations, which provides a better representation of the conservative laws for mass, momentum, and transport in the coastal region with complex geometry and bottom bathymetry. The model performance was firstly quantified with skill assessment statistics on the choice of different parameters and validated with observed tidal elevation, current velocity, direction and salinity data over a spring–neap tidal cycle collected in 2006. Numerical results show that the model with wetting–drying capability successfully simulated the tidal currents and salinity fields with a reasonable accuracy and indicate that the Oujiang River Estuary is a macrotidal estuary with strong tidal mixing. In addition, the model results also show that the Oujiang River Estuary is a well-mixed estuary during spring tide. Then, the numerical simulations were performed to compare the hydrodynamic process and salinity distribution before and after a river training, which was conducted by blocking the south branch of the Oujiang River mouth. The results reveal that with the only north access to the sea, the influence of the blocking project on the flood discharge capacity is limited and the incremental velocity is beneficial to the navigation channel maintenance, although it will cause some scour to the embankment. Furthermore, the redistribution of tidal prism passing in or out the north branch makes a little severe salinity intrusion during high tide or low tide. However, the salinity intrusion is still within acceptable range, although it can cause some adverse effect on water intaking of production and life. The variations of salinity levels in Yueqing Bay situated at the north of the river mouth are not obvious, so the blocking project will not bring damage to local aquiculture. However, significant changes of salinity happen inside or outside of the south branch, so enough attention need to be paid to the changes of environment caused by the salinity variation after the blocking project. Overall, by weighing advantages and disadvantages of the blocking project, it is feasible and the model can be considered as a tool for managing and studying estuarine circulation.