Hydrodynamic and morphological processes become more complex with large spatial variations after tidal barrier building and estuary restoration. Using a process-based model, responses in the estuary to a two-phase restoration measure in the Shuanglong Estuary are investigated. Numerical modeling indicates that tide-asymmetry in the barraged estuary is the primary factor that determines responses of morphology. After partial absence of tidal flats (first-phase restoration), flood tide-asymmetry is switched to ebb tide-asymmetry in the lower unrestored reach. This induces lower estuary erosion via increased tidal prism, though it is enhanced in the upper widened-deepened restored reach leading to severe siltation. After full restoration (second-phase restoration), current velocities are significantly increased with reduced flood tide-asymmetry. A quantitative comparison of the impact of the cross-sectional profile to net sediment transport shows that a switch from flood-dominated estuary to ebb-dominated estuary can be caused by reshaping the tidal flat which may reduce flood tide-asymmetry. The sediment flushing efficiency after the estuary restoration is further investigated in different sluice discharges with regards to two floodgate operations. Low sluice discharge during ebb tides increases the sediment flushing efficiency, but continuous high sluice discharge contributes to significant improvement of sediment flushing capacity and reduction of flushing duration. We conclude to prevent the flushed sediment from re-deposition into the estuary, a larger flushing capacity discharge released in a short period is required after the second-phase restoration in the Shuanglong Estuary.