ABSTRACT Taiwan is located at the seismic belt around Pacific Ocean. Earthquake occurs with high frequency and all kinds of degrees of typhoons also attack Taiwan almost every year. It causes serious destruction to the wharf structure. To ensure the safety of wharf structure subjected to earthquake and waves, a better knowledge about the interaction between structure and soil behavior is important. Not only is the interaction of solid and fluid concerned, but also the radiation condition of soil extending to infinite domain is considered. First, the research establishes the mass matrix and the stiffness matrix of dynamic equation, then applied to harbor system with the consistent infinitesimal finite element cell method. To efficiently simulate the radiation condition of soil the theory of similarity is employed. In reality, energy passes outward with soil extension, and changes every time. So we must calculate the value of energy passing on boundary at any time. Finally, adding the force of earthquake to the external force, the dynamic analysis is carried out in time-domain by using Newmark method.