An unstructured grid, Finite Volume Coastal Ocean Model (FVCOM) is used to study hydrodynamics and large-scale structure impacts in Changjiang Estuary. Field measurements conducted after the construction of the large-scale channel–jetty system are used to assess numerical results. The agreements between simulated and measured water levels, depth-averaged current velocities and tidally averaged longitudinal salinity distributions are excellent, as indicated by predictive skills higher than 0.94. The predictive skills for time series of salinity show a large range, from 0.97 to 0.62, in different measurement locations. The impacts of two 50 km long jetties and tens of spurs on the estuarine circulations as well as salinity distribution are investigated using comparisons of numerical results with and without jetty structures. Results reveal that the jetty structures intensify currents in the navigation channel and generate strong shear and vortices in jetty–spur blocks, which enhance turbulent mixing and degrade salinity stratification in the channel. The large-scale structures not only affect the flow field in the northern passage, but also play an important role in redistributing freshwater runoff in the multi-channel system, resulting in estuary-scale adjustments of circulations and salinity distribution.