Seismic analysis of pier type quay wall and caisson type quay wall was performed using FLAC 3D Which is a finite difference analysis program capable of total stress analysis and effective stress analysis and structural displacement and seismic risk were compared with each other. In order to consider the effective stress effect, the pore pressure of the ground was distributed, using Byrne(1991) simple formula to estimate parameter and applied to the finn model. Finally, in order to assessment of probabilistic seismic risk the seismic fragility curve of the quay wall was calculated and seismic hazrd of the structure installation area was considered simultaneously. Through the results of seismic risk analysis according to the total stress and effective stress analysis method, the necessity of effective stress analysis in the seismic design of the quay wall installed on the soft ground was confirmed.