Abstract: Global estuaries are currently undergoing a transition from large-scale development to natural ecological restoration, with the reshaping of hydrodynamics and geomorphology serving as the core of estuarine restoration. However, against the backdrop of drastic changes in estuarine dynamic environments, there is a lack of reasonable evaluation methods for the effects of multi-stage restoration projects in weak-dynamic estuaries. Taking the Luanhe River Estuary—a typical micro-tidal estuary—as the research object, this study simulates and analyzes the response characteristics of indicators including flow field, tidal prism, and sediment erosion and deposition following reclamation and multi-stage restoration projects to quantify the engineering effects. The results demonstrate that with the advancement of multi-stage projects returning aquaculture ponds to tidal flats, the high-velocity area of the estuary shrinks, and the maximum flow velocity decreases from 1.2 m/s to 0.6 m/s. The estuarine tidal prism and flood discharge capacity can be enhanced by 292% and 25%, respectively. The geomorphological evolution transitions from an "erosional" pattern to a benign trend characterized by "outer erosion and inner deposition," with the overall erosion-deposition intensity stabilizing between 0.1 and 0.15 m/a. This essentially establishes hydrodynamic conditions conducive to the self-maintenance of tidal flat wetlands. Furthermore, the spatial layout of restoration projects significantly influences the outcomes. Widening the channel inside the river mouth yields limited effects, while opening only one side of the mouth poses a hidden risk of local hydrodynamic imbalance. A comparison of multiple scenarios indicates that symmetrical restoration on both banks achieves superior results across indicators such as hydrodynamics, tidal prism, flood control, and erosion-deposition intensity. Additionally, variations in upstream water and sediment discharges have led to sediment starvation in the estuary. Merely restoring the estuarine dynamic environment is insufficient to drive the ecosystem to spontaneously evolve back to its pre-reclamation state, and the restored tidal flats face the risk of re-erosion. Therefore, synergistic management measures combining reservoir regulation and vegetation-based beach stabilization are required.