The general layout of the deep-water berth in sea island geography should consider some essentials, such as the berth form, the berth front-line position, berth length and wharf elevation. In order to improve the sea flow state and cover conditions, one important thing is the study of the complex hydrodynamic condition. We shall also consider other factors including the berthing stability, berthing & departing, technology, ship type combination, cost and so on. Based on the engineering projects, we suggest a reliable method, i.e. the multi-factor dynamic analysis method, to determine the most economical and reasonable general layout in sea island topography.