To explore the influence of the collecting and dispatching ratio of container water-water transshipment on the layout pattern of automated container stacking yard in the automated container terminal project with berths arranging perpendicularly to the shoreline,on the basis of the typical handling process model and layout applied generally in the domestic automated container terminals,we carry out a 3D simulation on two kinds of layout patterns by the software Flexterm,i.e.，the container stacking yard being perpendicular or parallel to the wharf shoreline.By analyzing the horizontal distance of the transport equipment and the influence on the operation efficiency under the two kinds of layout patterns of the container stacking yard,we summarize the adaptability of the two layout patterns for the automated container terminal project which is arranged perpendicularly to the wharf shoreline,to provide a theoretical basis for the design of similar automated container terminal engineering.