The tidal asymmetry-induced siltation below tidal barriers is a worldwide problem that restricts regional socio-economic and environmental development. The hydrodynamic processes of the small mud estuary also feature a high uncertainty after estuary restoration measures. In this study, a hydrodynamic model based on the MIKE21 is used to quantify the responses of tidal asymmetry to a two-phase restoration project in Shuanglong Estuary, Bohai Bay, China. According to the numerical modeling results, the tidal flat removal in the upper estuary (first-phase restoration) induces the flood asymmetry switching to the ebb asymmetry in unrestored reach but enhances flood asymmetry in widening restored reach. Although the tidal asymmetry reverts to flood-dominated pattern after full restoration over the estuary, the imbalance between flood and ebb velocities is relieved. A possible net sediment transport pattern based on a comparison of dominant asymmetric current and actual sediment transport period shows net sediments in the upper estuary and inlet transport seaward and landward, respectively, in the first-phase restoration, whereas landward net sediment transport occurs in the whole estuary under the second-phase restoration scenario. Given these results, we assume that a switch from the flood-dominated estuary to ebb-dominated estuary can be caused by redesigning the cross-sectional profile. The quantitative comparison of Lagrangian residual currents also implies that a channel–shoal structure rather than a flat bathymetry can promote the mass transport. Therefore, reshaping the channel–tidal flat system in restoration projects can prevent the sedimentation of the estuary and improve the water environment.