In this study, we present an integrated numerical model for sedimentation by long waves and also investigate morphological changes by far-field tsunami impacts. A set of models, each of which is responsible for hydrodynamics, sediment transport and morphological evolutions, are introduced with a basic concept of morphodynamic physics and are fully connected through two-way approach. Finite volume scheme, which turns out to be stable and suitable for long-term(more than 10 hours) tsunami simulations is used in the numerical discretization. An accuracy and applicability of developed model is evaluated through numerical tests covering one-dimensional or two-dimensional sedimentation problems in the shallow region. Then, we applied developed model to a field-scale tsunami, which had caused a significant bathymetric changes in harbors.