The morphology in the Liaodong Bay has undergone a marked change over the past decades due to the cutoff of nearby rivers. The fine sediment of the bay consists of both non-cohesive and cohesive fractions with relatively small particles over the seabed. Thus, a three-dimensional morphodynamic model accounting for non-cohesive and cohesive fractions is established to investigate the morphological change without sediment input from nearby rivers. A representative wave is chosen to compute the wave distribution in the Liaodong Bay and depth-dependent wave radiation stresses are employed by the hydrodynamic model. The advection-diffusion equation is used to simulate the fine sediment transport under the representative wave and tidal currents. The erosion flux of non-cohesive and cohesive sediment is taken into account. The simulated results of tidal level, velocities, directions, and sediment concentrations are in agreement with the measured data. The results demonstrate that the present model, which takes the erosion flux of both non-cohesive and cohesive fractions into account, gives more reasonable values than when accounting for cohesive sediment alone. When the three-dimensional morphodynamic model is applied to predict morphological change over the course of a year, the deposition is shown to be relatively small and the range of the erosion is increased compared to previous results of sediment input from the river. It can be concluded that the erosion in the Liaodong Bay is increasing due to the cutoff of the river, and that morphological evolution must be taken into account if any type of coastal construction plans are to be carried out over the seabed.