Caused by human activities, lagoon deposition, water area reduction and water quality deterioration of Qilihai Lagoon Wetland (QLW) become serious. Through the ecological restoration project of QLW (phase I), lagoon ecological environment will be improved by dredging project. Based on triple nested unstructured grids, the hydrodynamic and transport models of QLW were validated through observation data of tidal level, velocity magnitude and direction. Combined with the average residence time and the distribution of residence time in the whole basin calculated by Eulerian method and numerical simulation, the impact of dredging project on hydrodynamic and water exchange of QLW were analyzed. The results revealed that (1) the project had slight influence on tidal level, discharge and current speed during flood tide and ebb tide at the mouth of tidal inlet both increase after the dredging project; (2) the tidal prism of lagoon was increased by 87% after the dredging project, residence time was reduced by 38%, water exchange capacity was gradually weakened from tidal inlet to inner of lagoon and the main areas of water exchange improvement by the dredging project were water channel and center of lagoon; (3) the distribution of residence time before the project was mainly influenced by lagoon geomorphology, however, due to the water depth increases after the project, the flow field was less affected by geomorphology, and the distribution of water exchange capacity was mainly affected by the lagoon flow field. Improvement of water exchange capacity and ecological environment of QLW could be achieved efficiently by dredging project.