The study is aimed at developing a two-dimensional depth-averaged numerical model for bed evolution in the estuary-sea area, and, moreover, at simulating the long-term morphological change in the estuary and the nearby sea. To evaluate accuracy and practicability of the numerical simulation, physical hydraulic model experiments were performed. Waves in three scenarios, a summer period, a winter period, as well as a typhoon period, were adopted experimentally. Design conditions of the physical model were based on field observation of waves, tides, and bed elevation. Overall, the experimental results agree with those of the numerical simulation except those in deeper sea and some local regions. We conclude that the numerical model is applicable and reasonable for simulating the bed evolution in the estuary-sea area for engineering practices on construction planning and design.